{"studies":[{"source":"ARRAYEXPRESS","accession":"E-MTAB-12826","agent_decision":"include_canonical","extraction_status":"ok","title":"RNA-seq of ileal resection margins of ulcerative colitis patients that had total colectomy and ileal pouch anal anastomosis","summary":"We previously showed that abnormal morphology phenotype of ileal Paneth cells (Paneth cell phenotype [PCP]; as a surrogate for PC function) correlate with genetics, microbiota compositions, and aggressive outcome in Crohn’s disease (CD) patients. Given the shared genetics and clinical features between CD and ulcerative colitis (UC), we hypothesized that abnormal PCP also negatively modulates UC outcomes. As PCs has the highest density in the ileum, we further hypothesized that abnormal PCP from the terminal ileum could increase the risk of development of pouch complications after UC total colectomy and ileal pouch anal anastomosis (IPAA).","study_type_class":"target_rnaseq","technology_field":"BioStudies Source Characteristics","target_sample_rows":55,"included_by_policy_rows":55,"raw_sample_rows":55,"default_region_counts_json":"[{\"accession\": \"E-MTAB-12826\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"55\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"55\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2025-01-01","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-2967","agent_decision":"include_canonical","extraction_status":"ok","title":"Genome wide pathway analysis using gene expression data of colonic mucosa in patients with Inflammatory Bowel Disease","summary":"To provide new steps on the role of altered gene expression in the pathogenesis of these diseases, we performed whole gene expression profiling by comparing the RNA from inflamed and non-inflamed colonic mucosa","study_type_class":"target_expression_array","technology_field":"BioStudies Source Characteristics","target_sample_rows":58,"included_by_policy_rows":0,"raw_sample_rows":58,"default_region_counts_json":"[{\"accession\": \"E-MTAB-2967\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"15\", \"other_control\": \"0\", \"other_uc\": \"14\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"15\", \"total_control\": \"0\", \"total_uc\": \"14\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2014-11-30","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-5464","agent_decision":"include_canonical","extraction_status":"ok","title":"RNA sequencing of purified intestinal epithelial cells from paediatric biopsies including Inflammatory Bowel Disease and healthy controls","summary":"This study investigated alterations in the transcriptomic profiles of intestinal epithelial cells in Inflammatory Bowel Diseases (IBD), i.e. Crohn's Disease and Ulcerative Colitis.  Biopsies were taken from treatment-naive paediatric patients at diagnostic endoscopy from terminal ileum (TI), ascending colon (AC) and sigmoid colon (SC). Intestinal epithelial cells were purified using enzyme digestion and magnetic bead separation. RNA extraction was performed on EpCAM-positive cells, using AllPrep DNA/RNA mini kit.  An Agilent Bioanalyzer was used to check RNA integrity following the manufacturer’s guidelines. mRNA was sequenced at the University of Kiel, Germany.","study_type_class":"target_rnaseq","technology_field":"BioStudies Source Characteristics","target_sample_rows":79,"included_by_policy_rows":47,"raw_sample_rows":79,"default_region_counts_json":"[{\"accession\": \"E-MTAB-5464\", \"ascending_cd\": \"2\", \"ascending_control\": \"5\", \"ascending_uc\": \"3\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"3\", \"ileum_control\": \"10\", \"ileum_uc\": \"1\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"6\", \"sigmoid_control\": \"10\", \"sigmoid_uc\": \"7\", \"total_cd\": \"11\", \"total_control\": \"25\", \"total_uc\": \"11\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2017-10-16","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-7914","agent_decision":"include_canonical","extraction_status":"ok","title":"A multi-omics approach to understand and predict therapeutic success of anti-TNF and anti-integrin agents in inflammatory bowel disease","summary":"In this study we wanted to identify baseline predictors of successful anti-TNF and vedolizumab therapy in patients with inflammatory bowel disease (based on tissue transcriptomics and CD4/CD14 transcriptomics)","study_type_class":"target_rnaseq","technology_field":"BioStudies Source Characteristics","target_sample_rows":117,"included_by_policy_rows":41,"raw_sample_rows":314,"default_region_counts_json":"[{\"accession\": \"E-MTAB-7914\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"41\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"34\", \"other_control\": \"0\", \"other_uc\": \"42\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"75\", \"total_control\": \"0\", \"total_uc\": \"42\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2023-10-31","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-9658","agent_decision":"include_canonical","extraction_status":"ok","title":"Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease","summary":"Using RNA-seq we aimed to characterise the transcriptome of patients with PSC-associated IBD relative to patients with ulcerative colitis or healthy. This was performed across multiple tissue locations in order to define tissue-dependent associations.","study_type_class":"target_rnaseq","technology_field":"BioStudies Source Characteristics","target_sample_rows":82,"included_by_policy_rows":27,"raw_sample_rows":82,"default_region_counts_json":"[{\"accession\": \"E-MTAB-9658\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"11\", \"ileum_uc\": \"16\", \"other_cd\": \"0\", \"other_control\": \"21\", \"other_uc\": \"34\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"32\", \"total_uc\": \"50\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2021-01-01","source_date_kind":"release_date"},{"source":"CELLXGENE","accession":"5C868B6F-62C5-4532-9D7F-A346AD4B50A7","agent_decision":"include_canonical","extraction_status":"ok","title":"The landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colon","summary":"Crohn’s disease (CD) is a chronic gastrointestinal disease that is increasing in prevalence worldwide. CD is multifactorial, involving the complex interplay of genetic, immune, and environmental factors, necessitating a system-level understanding of its etiology. To characterize cell-type-specific transcriptional heterogeneity in active CD, we profiled 720,633 cells from the terminal ileum and colon of 71 donors with varying inflammation status. Our integrated datasets revealed organ- and compartment-specific responses to acute and chronic inflammation; most immune changes were in cell composition, whereas transcriptional changes dominated among epithelial and stromal cells. These changes correlated with endoscopic inflammation, but small and large intestines exhibited distinct responses, which were particularly apparent when focusing on IBD risk genes. Finally, we mapped markers of disease-associated myofibroblast activation and identified CHMP1A, TBX3, and RNF168 as regulators of fibrotic complications. Altogether, our results provide a roadmap for understanding cell-type- and organ-specific differences in CD and potential directions for therapeutic development.","study_type_class":"target_single_cell_rnaseq","technology_field":"CELLxGENE H5AD /obs grouped by biological sample","target_sample_rows":378,"included_by_policy_rows":220,"raw_sample_rows":378,"default_region_counts_json":"[{\"accession\": \"5C868B6F-62C5-4532-9D7F-A346AD4B50A7\", \"ascending_cd\": \"0\", \"ascending_control\": \"3\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"6\", \"descending_uc\": \"0\", \"ileum_cd\": \"41\", \"ileum_control\": \"155\", \"ileum_uc\": \"0\", \"other_cd\": \"14\", \"other_control\": \"144\", \"other_uc\": \"0\", \"sigmoid_cd\": \"9\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"64\", \"total_control\": \"314\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"6\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2023-03-31","source_date_kind":"publication_date"},{"source":"CELLXGENE","accession":"E33FFCD3-7CBF-4B8C-B0F4-85587AD5019A","agent_decision":"include_canonical","extraction_status":"ok","title":"Cells of the human intestinal tract mapped across space and time","summary":"The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. To comprehensively map cell lineages in the healthy developing, pediatric and adult human gut from ten distinct anatomical regions, as well as draining lymph nodes, we used single cell RNA-seq and VDJ analysis of roughly one third of a million cells. This reveals the presence of BEST4+ absorptive cells throughout the human intestinal tract, demonstrating the existence of this cell type beyond the colon for the first time. Furthermore, we implicate IgG sensing as a novel function of intestinal tuft cells, and link these cells to the pathogenesis of inflammatory bowel disease. We define novel glial and neuronal cell populations in the developing enteric nervous system, and predict cell-type specific expression of Hirschsprung’s disease-associated genes. Finally, using a systems approach, we identify key cell players across multiple cell lineages driving secondary lymphoid tissue formation in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. These data provide an unprecedented catalogue of intestinal cells, and new insights into cellular programs in development, homeostasis and disease.","study_type_class":"target_single_cell_rnaseq","technology_field":"CELLxGENE H5AD /obs grouped by biological sample","target_sample_rows":105,"included_by_policy_rows":53,"raw_sample_rows":113,"default_region_counts_json":"[{\"accession\": \"E33FFCD3-7CBF-4B8C-B0F4-85587AD5019A\", \"ascending_cd\": \"0\", \"ascending_control\": \"4\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"3\", \"descending_uc\": \"0\", \"ileum_cd\": \"7\", \"ileum_control\": \"27\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"52\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"7\", \"sigmoid_uc\": \"0\", \"total_cd\": \"7\", \"total_control\": \"98\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"5\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2022-09-15","source_date_kind":"publication_date"},{"source":"CELLXGENE","accession":"F11CB29C-B546-4738-9BD8-66EA621A7BD5","agent_decision":"include_canonical","extraction_status":"ok","title":"Single-cell integration reveals metaplasia in inflammatory gut diseases","summary":"The gastrointestinal tract is a multi-organ system crucial for efficient nutrient uptake and barrier immunity. Advances in genomics and a surge in gastrointestinal diseases1,2 has fuelled efforts to catalogue cells constituting gastrointestinal tissues in health and disease3. Here we present systematic integration of 25 single-cell RNA sequencing datasets spanning the entire healthy gastrointestinal tract in development and in adulthood. We uniformly processed 385 samples from 189 healthy controls using a newly developed automated quality control approach (scAutoQC), leading to a healthy reference atlas with approximately 1.1 million cells and 136 fine-grained cell states. We anchor 12 gastrointestinal disease datasets spanning gastrointestinal cancers, coeliac disease, ulcerative colitis and Crohn’s disease to this reference. Utilizing this 1.6 million cell resource (gutcellatlas.org), we discover epithelial cell metaplasia originating from stem cells in intestinal inflammatory diseases with transcriptional similarity to cells found in pyloric and Brunner’s glands. Although previously linked to mucosal healing4, we now implicate pyloric gland metaplastic cells in inflammation through recruitment of immune cells including T cells and neutrophils. Overall, we describe inflammation-induced changes in stem cells that alter mucosal tissue architecture and promote further inflammation, a concept applicable to other tissues and diseases.","study_type_class":"target_single_cell_rnaseq","technology_field":"CELLxGENE H5AD /obs grouped by biological sample","target_sample_rows":2643,"included_by_policy_rows":1002,"raw_sample_rows":3820,"default_region_counts_json":"[{\"accession\": \"F11CB29C-B546-4738-9BD8-66EA621A7BD5\", \"ascending_cd\": \"0\", \"ascending_control\": \"61\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"32\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"690\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"1134\", \"other_uc\": \"22\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"124\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"2136\", \"total_uc\": \"22\", \"transverse_cd\": \"0\", \"transverse_control\": \"95\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2025-10-27","source_date_kind":"publication_date"},{"source":"GEO","accession":"GSE100833","agent_decision":"include_canonical","extraction_status":"ok","title":"A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Microarray Analysis of Human Blood and Intestinal Biopsy Samples from a Phase 2b, Double-blind, Placebo-controlled Study of Ustekinumab in Crohn's Disease","summary":"Microarray Analysis of Human Whole Blood and Intestinal Biopsy Samples from a Phase 2b, Multicenter, Randomized, Double-blind, Placebo-controlled, Parallel-group Study of Ustekinumab in Crohn’s Disease","study_type_class":"target_expression_array","technology_field":"GEO SOFT series/platform metadata","target_sample_rows":844,"included_by_policy_rows":153,"raw_sample_rows":1717,"default_region_counts_json":"[{\"accession\": \"GSE100833\", \"ascending_cd\": \"26\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"20\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"64\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"36\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"22\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"189\", \"total_control\": \"0\", \"total_uc\": \"0\", \"transverse_cd\": \"21\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2017-07-07","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE101794","agent_decision":"include_canonical","extraction_status":"ok","title":"Age-of-Onset Dependent Immune maturation in Pediatric Crohn Disease","summary":"Purpose: To clarify the biological processes underlying variation in disease location and antimicrobial sero-reactivity across age-of onset in pediatric Crohn disease. Methods: We characterize the ileal global pattern of gene expression using single-end, 50bp RNA-sequencing using the Illumina HiSeq2000 in 304 treatment-naïve pediatric Crohn patients and non-IBD controls. Reads were quantified using Kallisto with Gencodev23 annotations. For all analyses, data were stratified by patient age-of-onset. Results: Performing differential analysis of all reasonably-expressed transcripts (TPM>5 in ≥5 samples, with significance defined as FDR-corrected p-value<0.05 and fold change≥1.5), we identify a robust gene signature with higher expresison of an immune gene set in older patients (≥10 years at diagnosis) compared to younger patients (<10 years at diagnosis), and a decrease in expression of antimicrobial Paneth cell-derived α-defensins. Conclusion: We provide evidence for maturation of mucosal Th1 immune response and loss of epithelial antimicrobial α-defensins with increasing age-of-onset.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":304,"included_by_policy_rows":304,"raw_sample_rows":304,"default_region_counts_json":"[{\"accession\": \"GSE101794\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"254\", \"ileum_control\": \"50\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"254\", \"total_control\": \"50\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2018-08-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE102134","agent_decision":"include_canonical","extraction_status":"ok","title":"Mucosal miRNA and gene expression profiling in ileum of patients with Crohn's disease","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":77,"included_by_policy_rows":12,"raw_sample_rows":120,"default_region_counts_json":"[{\"accession\": \"GSE102134\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"12\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"12\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2019-03-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE105074","agent_decision":"include_canonical","extraction_status":"ok","title":"Elevation in cell cycle and protein metabolism gene transcription in inactive colonic tissue from Icelandic patients with ulcerative colitis","summary":"BACKGROUND & AIMS: Ulcerative colitis (UC) is a chronic relapsing inflammatory disorder that affects the colonic epithelium. A combination of genetic and environmental factors is thought to be involved in the pathogenesis, resulting in an abnormal immune response and destruction of the colonic epithelium. In Iceland, the incidence of UC is one of the highest in the world and is three times more common than Crohn’s disease. Previous studies have suggested a genetic component may have an influence on the increased incidence. The aim of this study was to characterise a cohort of patients with UC and identify potential germ line mutations and pathways which could be associated with UC in this population. METHODS: We performed exome sequencing of genomic DNA and genome-wide microarray analysis on macroscopically non-inflamed colonic mucosa from Icelandic patients with UC and age and sexed matched controls. Gene-ontology analysis was used to identify common processes and pathways differentially expressed in tissue from UC cases. Exome sequence data were examined for very rare or novel mutations which might be over represented in the UC cohort. Combined matching of variant analysis and downstream influence on transcriptomic expression in the rectum was also analysed. RESULTS: Non-inflamed colonic tissue from patients with UC demonstrated a significant alteration in the transcriptomic profile compared to controls. Over 2,000 genes were differentially expressed in rectal tissue from UC patients and gene ontology analysis identified an up-regulation in genes associated with cell cycle control and protein processing in the endoplasmic reticulum. Exome sequencing identified two missense mutations in thiopurine S-methyltransferase (TPMT) with a minor allele frequency of 0.22 in the UC patients compared to a reported 0.062 in the Icelandic population and 0.03 in the non-Finnish European populations. A predicted damaging mutation in the inflammatory bowel disease associated gene SLC26A3 was identified which was associated with increased expression of DUOX2 and DUOXA2 in UC rectal tissue. CONCLUSIONS: In patients with UC, the colonic mucosa demonstrates a clear alteration in gene expression compared to control subjects. There is evidence of an elevation in genes involved with cell proliferation and the processing of proteins within the endoplasmic reticulum. Exome sequencing identified an increased prevalence of two damaging TPMT variants within the Icelandic UC population, which would suggest screening the UC population prior to initiation of therapy is warranted in order to avoid the serious toxicity associated with these mutations and azathioprine treatment.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":57,"included_by_policy_rows":27,"raw_sample_rows":57,"default_region_counts_json":"[{\"accession\": \"GSE105074\", \"ascending_cd\": \"0\", \"ascending_control\": \"15\", \"ascending_uc\": \"12\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"15\", \"other_uc\": \"15\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"30\", \"total_uc\": \"27\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2018-11-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE10616","agent_decision":"include_canonical","extraction_status":"ok","title":"Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC","summary":"Colon gene expression in human IBD. The three major clinical subsets of Inflammatory Bowel Disease (IBD) include colon-only Crohn's Disease (CD), ileo-colonic CD, and Ulcerative Colitis (UC). These experiments tested differential colon gene expression in these three types of IBD, relative to healthy control samples, and the local degree of mucosal inflammation as measured by the CD Histological Index of Severity (CDHIS). Colon biopsy samples were obtained from IBD patients at diagnosis and during therapy, and healthy controls. The global pattern of gene expression was determined using GeneSpring software, with a focus upon candidate genes identified in a recent genome wide association study in pediatric onset IBD. Data suggested that two of these candidate genes are up regulated in pediatric IBD, partially influenced by local mucosal inflammation. These experiments tested differential colon gene expression in healthy, CD, and UC samples for candidate genes identified in a recent pediatric onset IBD genome wide association study. Keywords: Single time point in CD and UC and healthy controls.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":58,"included_by_policy_rows":0,"raw_sample_rows":58,"default_region_counts_json":"[{\"accession\": \"GSE10616\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"32\", \"other_control\": \"16\", \"other_uc\": \"10\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"32\", \"total_control\": \"16\", \"total_uc\": \"10\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2009-03-11","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE107597","agent_decision":"include_canonical","extraction_status":"ok","title":"Ulcerative Colitis subjects","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":334,"included_by_policy_rows":128,"raw_sample_rows":334,"default_region_counts_json":"[{\"accession\": \"GSE107597\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"4\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"34\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"70\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"68\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"198\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"22\"}]","decision":"custom_override_required","source_date":"2018-04-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE108746","agent_decision":"include_canonical","extraction_status":"ok","title":"High-dimensional transcriptional analyses of UC Colon comparing RNALater to DMSO collection method","summary":"Simultaneous analyses of peripheral and mucosal immune compartments can yield insight into the pathogenesis of mucosal-associated diseases. Although methods to preserve peripheral immune cells are well established, studies involving mucosal immune cells have been hampered by lack of simple storage techniques. We provide a cryopreservation protocol allowing for storage of gastrointestinal (GI) tissue with preservation of viability and functionality of both immune and epithelial cells.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":72,"included_by_policy_rows":24,"raw_sample_rows":72,"default_region_counts_json":"[{\"accession\": \"GSE108746\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"4\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"12\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"10\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"36\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"10\"}]","decision":"baseline_ok","source_date":"2019-01-18","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE109142","agent_decision":"include_canonical","extraction_status":"ok","title":"Mucosal transcriptome of rectal biopsies in treatment-naïve, pediatric ulcerative colitits patients","summary":"Using recal mucosal biopsies, collected prior to treatment in new-onset pediatric ulcerative colitis patients, we performed RNAsequencing to generate transcriptomic profiles linked to pathogenesis, severity, and treatment response.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":226,"included_by_policy_rows":0,"raw_sample_rows":226,"default_region_counts_json":"[{\"accession\": \"GSE109142\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"20\", \"other_uc\": \"206\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"20\", \"total_uc\": \"206\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2018-11-27","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE111889","agent_decision":"include_canonical","extraction_status":"ok","title":"Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease","summary":"Purpose: The main Inflammatory Bowel Disease (IBD) Multi'omics Database (IBDMDB) study includes multi’omics measurements from over 100 subjects, sampled biweekly over up to a year in both adult and pediatric patients with IBD (Crohn’s disease and ulcerative colitis), along with non-IBD controls. Data types include fecal metagenomes, metatranscriptomes, metabolomes, and proteomes, as well as host genetics, intestinal biopsy transcriptomes, epigenetics, and 16S amplicon profiles. Subjects’ medical histories and demographics are collected at baseline and medication, diet, and disease activity profiled longitudinally. Methods: Methods: Total RNA was quantified using theQuant-iT™​ RiboGreen® RNA Assay Kit and normalized to 5ng/ul. Following plating, 2 uL of ERCC controls (using a 1:1000 dilution) were spiked into each sample. An aliquot of 200ng for each sample was transferred into library preparation which was an automated variant of​ ​the Illumina TruSeq™​ Stranded mRNA Sample Preparation Kit. This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample. It is followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 500bp cDNA then goes through library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using Broad designed indexed adapters substituted in for multiplexing. After enrichment the libraries were quantified using Quant-iT PicoGreen (1:200 dilution). After normalizing samples to 5 ng/uL, the set was pooled and quantified using the KAPA Library Quantification Kit for Illumina Sequencing Platforms. The entire process is in 96-well format and all pipetting is done by either Agilent Bravo or Hamilton Starlet. Pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the HiSeq 2000.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":250,"included_by_policy_rows":144,"raw_sample_rows":251,"default_region_counts_json":"[{\"accession\": \"GSE111889\", \"ascending_cd\": \"4\", \"ascending_control\": \"1\", \"ascending_uc\": \"3\", \"descending_cd\": \"4\", \"descending_control\": \"1\", \"descending_uc\": \"4\", \"ileum_cd\": \"47\", \"ileum_control\": \"21\", \"ileum_uc\": \"24\", \"other_cd\": \"54\", \"other_control\": \"24\", \"other_uc\": \"28\", \"sigmoid_cd\": \"13\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"9\", \"total_cd\": \"127\", \"total_control\": \"50\", \"total_uc\": \"73\", \"transverse_cd\": \"5\", \"transverse_control\": \"3\", \"transverse_uc\": \"5\"}]","decision":"baseline_ok","source_date":"2018-03-17","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE11223","agent_decision":"include_canonical","extraction_status":"ok","title":"Colon biopsies from UC patients and healthy controls","summary":"Transcriptional profiling of colon epithelial biopsies from ulcerative colitis patients and healthy control donors. Study aims to survey and analyze variation from disease in different GI regions. Keywords: disease state analysis","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":202,"included_by_policy_rows":132,"raw_sample_rows":202,"default_region_counts_json":"[{\"accession\": \"GSE11223\", \"ascending_cd\": \"0\", \"ascending_control\": \"17\", \"ascending_uc\": \"11\", \"descending_cd\": \"0\", \"descending_control\": \"22\", \"descending_uc\": \"19\", \"ileum_cd\": \"0\", \"ileum_control\": \"6\", \"ileum_uc\": \"1\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"24\", \"sigmoid_uc\": \"32\", \"total_cd\": \"0\", \"total_control\": \"69\", \"total_uc\": \"63\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2008-06-17","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE112366","agent_decision":"include_canonical","extraction_status":"ok","title":"Intestinal epithelial microvilli are abnormal in Crohn's disease","summary":"Biopsy samples (n=362) were collected from terminal ileum at baseline, 8 weeks after induction (Ustekinumab or placebo), and 44 weeks after maintenance (Ustekinumab 90 mg SC q12w, Ustekinumab 90 mg SC q8w, or placebo) therapies during endoscopy for RNA extraction and microarray analysis from patients with moderate-to-severe CD who participated in stelara CD phase 3 studies (UNITI-2 and IM-UNITI). These patients failed conventional therapies previously and largely naive to anti-TNF therpy. Ileum biopsies (n=26) collected from non-IBD subjects were also analyzed to serve as control. Enrichment of a core microvilli gene set was found to be reduced in UNITI-2 CD samples relative to controls, correlated with microvilli length and endoscopy score, and associated with response to treatment.","study_type_class":"target_expression_array","technology_field":"GEO SOFT series/platform metadata","target_sample_rows":388,"included_by_policy_rows":388,"raw_sample_rows":388,"default_region_counts_json":"[{\"accession\": \"GSE112366\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"362\", \"ileum_control\": \"26\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"362\", \"total_control\": \"26\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2019-03-20","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE115390","agent_decision":"include_canonical","extraction_status":"ok","title":"Differences in tissue immune cell populations following hematopoietic stem cell transplantation in Crohn’s disease patients","summary":"Treatment of severely refractory Crohn’s disease (CD) patients remains a clinical challenge. Recent studies show the efficacy of autologous hematopoietic stem cell transplant (HSCT) in these severely compromised patients. HSCT is thought to eliminate auto-reactive cells; however, no specific studies of immune reconstitution in CD patients are available. We studied a group of CD patients receiving autologous HSCT, with 50% of them achieving endoscopic drug-free remission. To elucidate the mechanism driving efficacy, we studied changes in the immune cell composition in tissue induced by HSCT.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":80,"included_by_policy_rows":0,"raw_sample_rows":80,"default_region_counts_json":"[{\"accession\": \"GSE115390\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"44\", \"other_control\": \"36\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"44\", \"total_control\": \"36\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2019-01-23","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE117993","agent_decision":"include_canonical","extraction_status":"ok","title":"Transcription profiles of rectal biopsies obtained during diagnostic colonoscopy for pediatric inflammatory bowel diseases.","summary":"RNA was isolated from rectal biopsies from 190 pediatric patients undergoing diagnostic colonoscopy for inflammatory bowel diseases, including Crohn's disease and ulcerative colitis. Single-end, 75-bp sequencing was performed, and raw reads aligned to the human genome using Gencode v 24 as reference. We included 14085 protein-coding mRNA genes in downstream analyses, where cutoffs of fold change>1.5 and FDR<0.05 were considered significant.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":190,"included_by_policy_rows":0,"raw_sample_rows":190,"default_region_counts_json":"[{\"accession\": \"GSE117993\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"92\", \"other_control\": \"55\", \"other_uc\": \"43\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"92\", \"total_control\": \"55\", \"total_uc\": \"43\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2018-11-27","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE120782","agent_decision":"include_canonical","extraction_status":"ok","title":"Microarray data generated from formalin-fixed, paraffin-embedded (FFPE) uninvolved small bowel (SB) ileal tissue.","summary":"Transcriptomic data was generated on uninvolved SB tissue from formalin-fixed paraffin-embedded (FFPE) small bowel resection margins of subjects requiring surgery at Cedars-Sinai Medical Center for Crohn’s disease.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":628,"included_by_policy_rows":0,"raw_sample_rows":628,"default_region_counts_json":"[]","decision":"custom_override_required","source_date":"2019-12-23","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE126124","agent_decision":"include_canonical","extraction_status":"ok","title":"Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease.","summary":"Presenting features of inflammatory bowel disease (IBD) are non-specific. We hypothesized that mRNA profiles could (1) identify genes and pathways involved in disease pathogenesis; (2) identify a molecular signature that differentiates IBD from other conditions; (3) provide insight into systemic and colon-specific dysregulation through study of the concordance of the gene expression. Children (8-18 years) were prospectively recruited at the time of diagnostic colonoscopy for possible IBD. We used transcriptome-wide mRNA profiling to study gene expression in colon biopsies and paired whole blood samples. Using blood mRNA measurements, we fit a regression model for disease state prediction that was validated in an independent test set of adult subjects (GSE3365). Results: Ninety-eight children were recruited [39 Crohn’s disease, 18 ulcerative colitis, 2 IBDU, 39 non-IBD]. There were 1,118 significantly differentially (IBD vs non-IBD) expressed genes in colon tissue, and 880 in blood. The direction of relative change in expression was concordant for 106/112 genes differentially expressed in both tissue types. The regression model from the blood mRNA measurements distinguished IBD vs non-IBD disease status in the independent test set with 80% accuracy using only 6 genes. The overlap of 5 immune and metabolic pathways in the two tissue types was significant (p<0.001). Conclusions: Blood and colon tissue from patients with IBD share a common transcriptional profile dominated by immune and metabolic pathways. Our results suggest that peripheral blood expression levels of as few as 6 genes (IL7R, UBB, TXNIP, S100A8, ALAS2, and SLC2A3) may distinguish patients with IBD from non-IBD. Ninety-eight children were recruited [39 Crohn’s disease, 18 ulcerative colitis, 2 IBDU, 39 non-IBD]. There were 1,118 significantly differentially (IBD vs non-IBD) expressed genes in colon tissue, and 880 in blood. The direction of relative change in expression was concordant for 106/112 genes differentially expressed in both tissue types. The regression model from the blood mRNA measurements distinguished IBD vs non-IBD disease status in the independent test set with 80% accuracy using only 6 genes. The overlap of 5 immune and metabolic pathways in the two tissue types was significant (p<0.001). Conclusions: Blood and colon tissue from patients with IBD share a common transcriptional profile dominated by immune and metabolic pathways. Our results suggest that peripheral blood expression levels of as few as 6 genes (IL7R, UBB, TXNIP, S100A8, ALAS2, and SLC2A3) may distinguish patients with IBD from non-IBD.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":78,"included_by_policy_rows":0,"raw_sample_rows":176,"default_region_counts_json":"[{\"accession\": \"GSE126124\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"37\", \"other_control\": \"20\", \"other_uc\": \"18\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"37\", \"total_control\": \"20\", \"total_uc\": \"18\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2019-10-29","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE13367","agent_decision":"include_canonical","extraction_status":"ok","title":"Genome-wide gene expression analysis of mucosal colonic biopsies and isolated colonocytes...","summary":"Background & Aims: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. Methods: Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n=8), quiescent UC (n=9), and with irritable bowel syndrome (controls, n=10). After isolation of colonocytes and subsequent extraction of total RNA, GWGE data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P11 software (Umetrics, Umeå, Sweden). Results: A clear separation between active UC, quiescent UC and control biopsies were found, whereas the model for the colonocytes was unable to distinguish between quiescent UC and controls. The differentiation between quiescent UC and control biopsies was governed by unique profiles containing gene expressions with significant fold changes. These primarily belonged to the family of homeostatic chemokines revealing a plausible explanation to the abnormal regulated innate immune response seen in patients with UC. Conclusion: This study has demonstrated the presence of a continuous inflammatory state in quiescent UC, which seems to reflect an altered gene expression profile of lamina propria cells. Keywords: Colonocytes, continuous inflammation, mucosal colonic biopsies, gene expression profiles","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":56,"included_by_policy_rows":36,"raw_sample_rows":56,"default_region_counts_json":"[{\"accession\": \"GSE13367\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"20\", \"descending_uc\": \"16\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"20\", \"total_uc\": \"16\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2009-09-16","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE134881","agent_decision":"include_canonical","extraction_status":"ok","title":"Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy","summary":"Purpose: IBD diagnosis correlation with failure to achieve corticosteroid-free durable remission upon anti-TNF therapy Results: Enrichment of the GIMATS module (unique cellular signature found in a small cohort of surgically resected iCD ileums by scRNAseq) was also present in early stages of disease, prior to any biological therapy Conclusion: Confirmed the presence of the GIMATS module in bulk expression dataset and revealed that the presence of the module at diagnosis is associated with failure to achieve durable corticosteroid-free remission upon anti-TNF therapy in a pediatric inception cohort","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":199,"included_by_policy_rows":13,"raw_sample_rows":199,"default_region_counts_json":"[{\"accession\": \"GSE134881\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"13\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"13\", \"total_control\": \"0\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2019-08-21","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE137344","agent_decision":"include_canonical","extraction_status":"ok","title":"Ileum Transcriptomic Profiling in Inflammatory Bowel Disease","summary":"We report ileum gene expression of 37 controls and 158 patients with either Crohn's disease (n=112), ulcerative colitis (n=44), unclassifed IBD (1), or IBS (1). We contrast gene expression in African American (n=104) versus white (n=25) CD and UC patients.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":195,"included_by_policy_rows":193,"raw_sample_rows":195,"default_region_counts_json":"[{\"accession\": \"GSE137344\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"112\", \"ileum_control\": \"37\", \"ileum_uc\": \"44\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"112\", \"total_control\": \"37\", \"total_uc\": \"44\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2020-04-15","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE139179","agent_decision":"include_canonical","extraction_status":"ok","title":"Differences in tissue populations following hematopoietic stem cell transplantation in Crohn’s disease patients","summary":"Treatment of severely refractory Crohn’s disease (CD) patients remains a clinical challenge. Recent studies show the efficacy of autologous hematopoietic stem cell transplant (HSCT) in these severely compromised patients. HSCT is thought to eliminate auto-reactive cells; however, no specific studies of immune reconstitution in CD patients are available. We studied a group of CD patients (n=18) receiving autologous HSCT and non-IBD patients (n=19) to elucidate the mechanism of interaction with the microorganisms.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":316,"included_by_policy_rows":144,"raw_sample_rows":316,"default_region_counts_json":"[{\"accession\": \"GSE139179\", \"ascending_cd\": \"14\", \"ascending_control\": \"36\", \"ascending_uc\": \"0\", \"descending_cd\": \"12\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"10\", \"ileum_control\": \"30\", \"ileum_uc\": \"0\", \"other_cd\": \"4\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"2\", \"sigmoid_control\": \"36\", \"sigmoid_uc\": \"0\", \"total_cd\": \"46\", \"total_control\": \"102\", \"total_uc\": \"0\", \"transverse_cd\": \"4\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2020-10-22","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE150961","agent_decision":"include_canonical","extraction_status":"ok","title":"Treatment Naïve and Follow-Up Pediatric Ulcerative Colitis Rectal Gene Expression","summary":"PROTECT is a multicenter pediatric inception cohort study of response to standardized colitis therapy. In order to more explicitly model progression to colectomy within one year of diagnosis, we performed differential expression analysis between baseline rectal RNAseq biopsies of 21 patients who progressed to colectomy, and 310 who did not. We report rectal gene expression of pediatric patients with ulcerative colitis at diagnosis and at one year follow-up.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":418,"included_by_policy_rows":0,"raw_sample_rows":418,"default_region_counts_json":"[{\"accession\": \"GSE150961\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"418\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"418\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2021-05-20","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE152321","agent_decision":"include_canonical","extraction_status":"ok","title":"Profiling intestinal T cell subsets and their dynamics in Crohn's disease after treatment with the anti-integrin therapeutic etrolizumab","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":1496,"included_by_policy_rows":0,"raw_sample_rows":1496,"default_region_counts_json":"[{\"accession\": \"GSE152321\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"6\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"6\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2021-07-23","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE153974","agent_decision":"include_canonical","extraction_status":"ok","title":"Targeted ileal transcriptomic analysis in paediatric IBDs.","summary":"We employed contemporary targeted autoimmune RNA sequencing (HTG molecular diagnostics, Autoimmune panel) to ileal tissue derived from 96 paediatric IBD, Crohn's disease, Ulcerative colitis patients and controls. Weighted-gene-co-expression-network-analysis (WGCNA) was performed and differentially expressed genes (DEGs) were determined. We integrated clinical data to determine co-expression modules associated with time to relapse.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":96,"included_by_policy_rows":92,"raw_sample_rows":96,"default_region_counts_json":"[{\"accession\": \"GSE153974\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"57\", \"ileum_control\": \"17\", \"ileum_uc\": \"18\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"57\", \"total_control\": \"17\", \"total_uc\": \"18\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2021-05-12","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE158952","agent_decision":"include_canonical","extraction_status":"ok","title":"Transcriptome Profiling of Rectal and Ileal Tissues in Inflammatory Bowel Disease","summary":"We report whole mRNA gene expression and Percent Spliced In (PSI) estimates for rectal (n=59) and ileal (n=60) tissue samples of 33 patients with either Crohn's disease (n=19) or ulcerative colitis (n=14)","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":119,"included_by_policy_rows":60,"raw_sample_rows":119,"default_region_counts_json":"[{\"accession\": \"GSE158952\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"32\", \"ileum_control\": \"0\", \"ileum_uc\": \"28\", \"other_cd\": \"33\", \"other_control\": \"0\", \"other_uc\": \"26\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"65\", \"total_control\": \"0\", \"total_uc\": \"54\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2020-10-08","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE165512","agent_decision":"include_canonical","extraction_status":"ok","title":"Characterization of the IL23-IL17 immune axis in IBD patients","summary":"The aim of this study is to investigate the molecular mechanisms of IL23-IL17 immune axis in IBD, with particular attention to its role in maintaining mucosal barrier integrity under both physiological and pathological conditions","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":170,"included_by_policy_rows":55,"raw_sample_rows":170,"default_region_counts_json":"[{\"accession\": \"GSE165512\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"44\", \"ileum_control\": \"11\", \"ileum_uc\": \"0\", \"other_cd\": \"40\", \"other_control\": \"35\", \"other_uc\": \"40\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"84\", \"total_control\": \"46\", \"total_uc\": \"40\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2021-11-26","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE166928","agent_decision":"include_canonical","extraction_status":"ok","title":"IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":95,"included_by_policy_rows":0,"raw_sample_rows":215,"default_region_counts_json":"[{\"accession\": \"GSE166928\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"19\", \"other_control\": \"42\", \"other_uc\": \"10\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"19\", \"total_control\": \"42\", \"total_uc\": \"10\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2021-07-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE16879","agent_decision":"include_canonical","extraction_status":"ok","title":"Mucosal expression profiling in patients with inflammatory bowel disease before and after first infliximab treatment","summary":"We used microarrays to identify mucosal gene signatures predictive of response to infliximab (IFX) in patients with inflammatory bowel disease (IBD) and to gain more insight into the pathogenesis of IBD. Keywords: drug response and treatment effect","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":133,"included_by_policy_rows":42,"raw_sample_rows":133,"default_region_counts_json":"[{\"accession\": \"GSE16879\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"36\", \"ileum_control\": \"6\", \"ileum_uc\": \"0\", \"other_cd\": \"37\", \"other_control\": \"6\", \"other_uc\": \"48\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"73\", \"total_control\": \"12\", \"total_uc\": \"48\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2009-11-03","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE169360","agent_decision":"include_canonical","extraction_status":"ok","title":"Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis","summary":"Due to the lack of clinical, immunologic, genetic and laboratory markers to predict remission without relapse, there is no clear recommendation regarding withdrawal of therapy. Therefore, this study was to investigate if transcriptional analysis together with Cox survival analysis might be able to reveal molecular markers that are specific for remission duration and outcome. Mucosal biopsies from patients in remission, with active treatment-naïve ulcerative colitis and healthy control subjects underwent whole-transcriptome RNA-seq. Principal component analysis (PCA) and Cox proportional hazards regression analysis was applied to the remission data concerning duration and status of patients. A randomly chosen remission sample set was used for validation of the applied methods and results. The analyses distinguished two different UC remission patient groups with respect to remission duration and outcome (relapse). Both groups showed that altered states of UC with quiescent microscopic disease activity still present. The patient group with the longest remission duration and no relapse revealed specific and increased expression of antiapoptotic factors belonging to the MTRNR2-like gene family and non-coding RNAs. In summary, the expression of anti-apoptotic factors and non-coding RNAs may contribute to personalized medicine approaches in UC by improving patient stratification for different treatment regimens.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":56,"included_by_policy_rows":0,"raw_sample_rows":56,"default_region_counts_json":"[{\"accession\": \"GSE169360\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"16\", \"other_uc\": \"40\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"16\", \"total_uc\": \"40\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2023-05-24","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE171770","agent_decision":"include_canonical","extraction_status":"ok","title":"Therapeutic IL-6 trans-signalling inhibition by olamkicept (sgp130Fc) in patients with active inflammatory bowel disease","summary":"Background A large unmet therapeutic need exists in inflammatory bowel diseases (IBD). Inhibition of interleukin (IL)-6 appears to be effective, but the therapeutic benefit of a complete IL-6/IL-6R blockade is limited by profound immunosuppression. Evidence has emerged, that chronic pro-inflammatory activity of IL-6 is mainly mediated by trans-signalling via a complex of IL-6 bound to soluble IL-6R engaging the gp130 receptor without the need of membrane bound IL6R. We have developed a decoy protein, sgp130Fc, which exclusively blocks IL-6 pro-inflammatory trans-signalling and has shown efficacy in preclinical models of IBD, without signs of immunosuppression. Methods We present a 12-week, open label, prospective phase IIa trial (FUTURE) in 16 patients with active IBD treated with the trans-signalling inhibitor olamkicept (sgp130Fc) to assess molecular mechanisms, safety and effectiveness of IL-6 trans-signalling blockade in vivo. We performed in-depth molecular profiling at various time points before and after therapy induction to identify the mechanism of action of olamkicept. Results Olamkicept was well tolerated and induced clinical response in 44% and clinical remission in 19% of patients. Clinical effectiveness coincided with target inhibition (reduction of phosphorylated STAT3) and marked transcriptional changes in the inflamed mucosa. An olamkicept-specific transcriptional signature, distinguishable from remission signatures of anti-TNF (infliximab) or anti-integrin (vedolizumab) therapies was identified. Conclusion Our data suggest that blockade of IL-6 trans-signaling holds large promise for the therapy of IBD and should undergo full clinical development as a new immunoregulatory therapy of IBD.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":176,"included_by_policy_rows":176,"raw_sample_rows":352,"default_region_counts_json":"[{\"accession\": \"GSE171770\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"76\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"100\", \"total_cd\": \"76\", \"total_control\": \"0\", \"total_uc\": \"100\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2021-04-10","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE179285","agent_decision":"include_canonical","extraction_status":"ok","title":"Embark cross-sectional study of inactive and active lesions from the ileum and colon of inflammatory bowel disease patients","summary":"Hypothesis: Gene expression differences in biopsies from patients with inflammatory bowel disease can be used to identify molecular heterogeneity within patients with active disease. Methods: Patients with a diagnosis of Crohn's disease, ulcerative colitis or normal healthy controls (with or without infectious colitis) underwent ileocolonoscopy. In healthy controls, biopsies were taken in the sigmoid colon (n=21), ascending/descending colon (n=25) and the terminal ileum (n=12). In patients with Crohn's disease, biopsies were taken in the ascending/descending colon (n=107) and terminal ileum (n=70) in uninflamed areas in all patients; in patients with mucosal lesions, additional biopsies were taken in inflamed regions of the ascending/descending colon (n=35) and terminal ileum (n=55). In ulcerative colitis patients, paired uninflamed sigmoid (n=48) and inflamed sigmoid biopsies (n=46) were taken. Biopsies were placed in RNAlater at the clinical site, frozen and shipped to Genentech, where they were disrupted using TissueLyzer beads, then RNA was isolated using RNeasy columns. RNA was hybridized to Agilent human 4x44kv1 arrays, dual channel, using universal reference.","study_type_class":"target_expression_array","technology_field":"GEO SOFT series/platform metadata","target_sample_rows":254,"included_by_policy_rows":101,"raw_sample_rows":254,"default_region_counts_json":"[{\"accession\": \"GSE179285\", \"ascending_cd\": \"14\", \"ascending_control\": \"12\", \"ascending_uc\": \"1\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"33\", \"ileum_control\": \"8\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"11\", \"sigmoid_uc\": \"22\", \"total_cd\": \"47\", \"total_control\": \"31\", \"total_uc\": \"23\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2021-07-26","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE183620","agent_decision":"include_canonical","extraction_status":"ok","title":"RNA sequencing of CD11b+ cells isolated from human gut mucosal biopsies of IBD patients","summary":"CD11b+ cells isolated from IBD patient biopsies have distinct transcriptomic signatures based on their location along the GI tract, inflammation status, IBD type, and medication response. These cells also respond to JAK inhibitors by decreasing cytokine output.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":58,"included_by_policy_rows":5,"raw_sample_rows":58,"default_region_counts_json":"[{\"accession\": \"GSE183620\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"5\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"2\", \"other_control\": \"0\", \"other_uc\": \"13\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"7\", \"total_control\": \"0\", \"total_uc\": \"13\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2022-08-23","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE184593","agent_decision":"include_canonical","extraction_status":"ok","title":"Transcriptional behavior of regulatory T cells predicts IBD patient responses to vedolizumab therapy","summary":"Vedolizumab (VDZ) is used to treat patients with IBD but the exact way it works is not known. We studied the immune system in the blood and intestine of patients treated with VDZ and found immune characteristics that correlated with response.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":67,"included_by_policy_rows":21,"raw_sample_rows":172,"default_region_counts_json":"[{\"accession\": \"GSE184593\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"16\", \"ileum_control\": \"0\", \"ileum_uc\": \"5\", \"other_cd\": \"16\", \"other_control\": \"0\", \"other_uc\": \"30\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"32\", \"total_control\": \"0\", \"total_uc\": \"35\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2022-08-23","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE186582","agent_decision":"include_canonical","extraction_status":"ok","title":"Expression data from intestinal mucosa of patients with Crohn disease","summary":"We used microarrays to detail the global signature of gene expression underlying endoscopic recurrence of CD and identified distinct gene signature predicting postoperative recurrence.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":978,"included_by_policy_rows":442,"raw_sample_rows":978,"default_region_counts_json":"[{\"accession\": \"GSE186582\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"392\", \"ileum_control\": \"50\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"392\", \"total_control\": \"50\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2021-12-05","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE191234","agent_decision":"include_canonical","extraction_status":"ok","title":"IBD HIBEC and HILEC transcriptome compendium","summary":"The study aims to investigate the differences between Human intestinal blood and lymphatic endothelial cells, HIBECs and HILECs, respectively, isolated from colon and ilea of IBD and control patients.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":54,"included_by_policy_rows":10,"raw_sample_rows":54,"default_region_counts_json":"[{\"accession\": \"GSE191234\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"6\", \"ileum_control\": \"4\", \"ileum_uc\": \"0\", \"other_cd\": \"14\", \"other_control\": \"14\", \"other_uc\": \"16\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"20\", \"total_control\": \"18\", \"total_uc\": \"16\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2021-12-21","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE193677","agent_decision":"include_canonical","extraction_status":"ok","title":"Biopsy expression profiling of an adult inflammatory bowel disease cohort","summary":"Inflammatory Bowel Disease (IBD) is a progressive disease of the gut and consists of two types, Crohn’s Disease (CD) and Ulcerative Colitis (UC). It is a complex disease involving genetic, microbial, and environmental factors. The incidence of IBD is steadily increasing and current therapeutic options are plateauing. Thus treatments are evolving to 1. deeper levels of remission from clinical to endoscopic and histologic normalization and 2. Embrace novel targets or drug combinations. We explored whole transcriptome data generated in biopsy specimens sampled from a large cohort of adult IBD and control subjects to provide 1. a granular, objective and sensitive molecular measures of disease activity in the gut and 2. Novel molecular mechanisms and biomarkers underlying IBD pathology.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":2490,"included_by_policy_rows":551,"raw_sample_rows":2490,"default_region_counts_json":"[{\"accession\": \"GSE193677\", \"ascending_cd\": \"35\", \"ascending_control\": \"18\", \"ascending_uc\": \"27\", \"descending_cd\": \"26\", \"descending_control\": \"6\", \"descending_uc\": \"46\", \"ileum_cd\": \"162\", \"ileum_control\": \"121\", \"ileum_uc\": \"0\", \"other_cd\": \"152\", \"other_control\": \"309\", \"other_uc\": \"161\", \"sigmoid_cd\": \"30\", \"sigmoid_control\": \"2\", \"sigmoid_uc\": \"48\", \"total_cd\": \"419\", \"total_control\": \"461\", \"total_uc\": \"293\", \"transverse_cd\": \"14\", \"transverse_control\": \"5\", \"transverse_uc\": \"11\"}]","decision":"baseline_ok","source_date":"2022-09-16","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE206171","agent_decision":"include_canonical","extraction_status":"ok","title":"Gene expression profiling of sigmoid colonic tissue form patients with ulcerative colitis and healthy controls","summary":"To assess mRNA gene expression levels in patients with ulcerative colitis (UC) and healthy controls.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":152,"included_by_policy_rows":119,"raw_sample_rows":152,"default_region_counts_json":"[{\"accession\": \"GSE206171\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"38\", \"sigmoid_uc\": \"81\", \"total_cd\": \"0\", \"total_control\": \"38\", \"total_uc\": \"81\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2024-07-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE206285","agent_decision":"include_canonical","extraction_status":"ok","title":"Efficacy and safety of ustekinumab treatment in patients with ulcerative colitis","summary":"UNIFI was a randomized placebo-controlled phase 3 clinical trial evaluating the efficacy and safety of ustekinumab (ClinicalTrials.gov Identifier: NCT02407236). Gene expression profiling by microarrays was carried out at baseline on biopsies from the sigmoid colon (15-20cm from anal verge) of patients (n=550) with moderate-to-severe ulcerative colitis and of healthy subjects (n=18). Ulcerative colitis patients received placebo (n=186) or ustekinumab (n=364). The effects of two different dosages were investigated: 130mg (n=180) and 6mg/kg (n=184).","study_type_class":"target_expression_array","technology_field":"GEO SOFT series/platform metadata","target_sample_rows":568,"included_by_policy_rows":568,"raw_sample_rows":568,"default_region_counts_json":"[{\"accession\": \"GSE206285\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"18\", \"sigmoid_uc\": \"550\", \"total_cd\": \"0\", \"total_control\": \"18\", \"total_uc\": \"550\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2022-08-08","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE207022","agent_decision":"include_canonical","extraction_status":"ok","title":"Efficacy and safety of ustekinumab treatment in patients with Crohn's disease","summary":"UNITI-2 was a phase 3 clinical trial (ClinicalTrials.gov Identifier: NCT01369342) comparing the effects (both positive and negative) of an initial treatment with ustekinumab to a placebo over 8 weeks in patients with moderately to severely active Crohn's disease.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":148,"included_by_policy_rows":0,"raw_sample_rows":148,"default_region_counts_json":"[{\"accession\": \"GSE207022\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"125\", \"other_control\": \"23\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"125\", \"total_control\": \"23\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2022-09-08","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE20881","agent_decision":"include_canonical","extraction_status":"ok","title":"Colon biopsies from Crohns patients and healthy controls","summary":"The aim of this study was to investigate differential intestinal gene expression in patients with Crohn's disease (CD) and controls. 172 biopsies from CD and control subjects were studied. Endoscopic biopsies were taken at ileocolonoscopy from five specific anatomical locations including the terminal ileum for RNA extraction.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":172,"included_by_policy_rows":114,"raw_sample_rows":172,"default_region_counts_json":"[{\"accession\": \"GSE20881\", \"ascending_cd\": \"10\", \"ascending_control\": \"17\", \"ascending_uc\": \"0\", \"descending_cd\": \"12\", \"descending_control\": \"23\", \"descending_uc\": \"0\", \"ileum_cd\": \"7\", \"ileum_control\": \"6\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"12\", \"sigmoid_control\": \"27\", \"sigmoid_uc\": \"0\", \"total_cd\": \"41\", \"total_control\": \"73\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2010-07-19","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE212849","agent_decision":"include_canonical","extraction_status":"ok","title":"Prediction of Golimumab Response in the PROgECT Phase 2a Open-Label Trial of Patients With Ulcerative Colitis","summary":"PROgECT (ClinicalTrials.gov Identifier: NCT01988961) was a multicenter, open-label study evaluating the accuracy of a probe-set panel in predicting response to golimumab treatment in participants with moderately to severely active ulcerative colitis (UC). Biopsy samples (collected 15 to 20 cm from the anal verge) were taken at screening from 84 patients and used for RNA extraction and profiling by microarrays. All patients enrolled in the study received the approved induction dose regimen of subcutaneous (SC) golimumab.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":84,"included_by_policy_rows":0,"raw_sample_rows":84,"default_region_counts_json":"[{\"accession\": \"GSE212849\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"84\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"84\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2022-09-08","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE215924","agent_decision":"include_canonical","extraction_status":"ok","title":"Small bowel RNA-seq data from patients with Crohn's disease and patients with colon cancer (non-CD controls)","summary":"To identify the dysregulated molecular pathways and core genes associated with the chronic and progressive course of CD, we evaluated the gene expression profiles of uninflamed small bowel tissues from CD patients who underwent small bowel resection and compared the results with those of patients with right colon cancer, who served as uninflamed non-CD controls.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":79,"included_by_policy_rows":70,"raw_sample_rows":79,"default_region_counts_json":"[{\"accession\": \"GSE215924\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"70\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"70\", \"total_control\": \"0\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2024-12-17","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE217352","agent_decision":"include_canonical","extraction_status":"ok","title":"A Blood-based Transcriptomic Signature Stratifies Severe Crohn's disease and Defines Potentially Targetable Therapeutic Pathways","summary":"Surgical resection in severe Crohn's disease is a common consequence of therapeutic failure. We identified 2 severe CD subtypes: one similar to non-IBD subjects, the other exhibited a mucosal-like gene signature, altered T-cell subsets, severity features and decreased pro-inflammatory expression post-surgery. These findings may identify targets for CD subtype-specific therapeutic and biomarker development.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":116,"included_by_policy_rows":0,"raw_sample_rows":265,"default_region_counts_json":"[{\"accession\": \"GSE217352\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"99\", \"other_control\": \"17\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"99\", \"total_control\": \"17\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2024-11-04","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE221161","agent_decision":"include_canonical","extraction_status":"ok","title":"​​​Developing biomarkers incorporating high throughput RNA, DNA, small RNA sequencing and protein expression in Inflammatory Bowel Disease using formalin-fixed, paraffin-embedded (FFPE) tissue samples.​​","summary":"This dataset includes RNA-seq data from ileal and colonic biopsies at time of diagnosis for treatment-naive, uncomplicated Crohn's disease (CD) patients and matched controls. This is includes 56 CD patients each for ileal and colonic tissue and for controls, 46 colonic samples and 45 ileal samples. Clinical characteristics such as development of complications, disease remission, or progression to surgery were recorded with a mean follow-up of 6 years.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":406,"included_by_policy_rows":202,"raw_sample_rows":406,"default_region_counts_json":"[{\"accession\": \"GSE221161\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"112\", \"ileum_control\": \"90\", \"ileum_uc\": \"0\", \"other_cd\": \"112\", \"other_control\": \"92\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"224\", \"total_control\": \"182\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2024-02-07","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE228122","agent_decision":"include_canonical","extraction_status":"ok","title":"Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects","summary":"The study was design to compare transcriptomic profiles of whole biopsies to enteroid/colonoid lines derived from them. In the accompanying publication, we observed substantial overlap of pathways upregulated in Crohn’s disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":58,"included_by_policy_rows":25,"raw_sample_rows":115,"default_region_counts_json":"[{\"accession\": \"GSE228122\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"6\", \"ileum_control\": \"15\", \"ileum_uc\": \"4\", \"other_cd\": \"7\", \"other_control\": \"15\", \"other_uc\": \"5\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"13\", \"total_control\": \"30\", \"total_uc\": \"9\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2023-08-22","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE230569","agent_decision":"include_canonical","extraction_status":"ok","title":"Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":226,"included_by_policy_rows":0,"raw_sample_rows":253,"default_region_counts_json":"[{\"accession\": \"GSE230569\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"92\", \"other_control\": \"60\", \"other_uc\": \"72\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"92\", \"total_control\": \"60\", \"total_uc\": \"72\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2023-04-30","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE234982","agent_decision":"include_canonical","extraction_status":"ok","title":"Vedolizumab efficacy is associated with decreased intracolonic dendritic cells, not memory T cells","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":192,"included_by_policy_rows":42,"raw_sample_rows":884,"default_region_counts_json":"[{\"accession\": \"GSE234982\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"40\", \"ileum_control\": \"0\", \"ileum_uc\": \"2\", \"other_cd\": \"86\", \"other_control\": \"0\", \"other_uc\": \"64\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"126\", \"total_control\": \"0\", \"total_uc\": \"66\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2023-08-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE235236","agent_decision":"include_canonical","extraction_status":"ok","title":"Bulk RNAseq expression data of colon biopsies from intestinal mucosa of non-IBD controls and patients with Crohn's disease or ulcerative colitis","summary":"Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in manifestations and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to explore the transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply single-cell RNA-sequencing to human inflamed intestine and show that the largest differences among patients are present within the myeloid compartment including macrophages and neutrophils. Using spatial transcriptomics in human tissue at single-cell resolution (CosMx Spatial Molecular Imaging) we spatially localized each of the macrophage and neutrophil subsets identified by single-cell RNA-sequencing and unravel further macrophage diversity based on their tissue localization. Finally, single-cell RNA-sequencing combined with single-cell spatial analysis reveals a strong communication network involving macrophages and inflammatory fibroblasts. Our data sheds light on the cellular complexity of these diseases and points towards the myeloid and stromal compartments as important cellular subsets for understanding patient-to-patient heterogeneity.","study_type_class":"target_spatial_transcriptomics","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":56,"included_by_policy_rows":47,"raw_sample_rows":56,"default_region_counts_json":"[{\"accession\": \"GSE235236\", \"ascending_cd\": \"3\", \"ascending_control\": \"0\", \"ascending_uc\": \"1\", \"descending_cd\": \"5\", \"descending_control\": \"0\", \"descending_uc\": \"1\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"5\", \"other_control\": \"0\", \"other_uc\": \"4\", \"sigmoid_cd\": \"7\", \"sigmoid_control\": \"8\", \"sigmoid_uc\": \"20\", \"total_cd\": \"22\", \"total_control\": \"8\", \"total_uc\": \"26\", \"transverse_cd\": \"2\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2023-06-20","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE236055","agent_decision":"include_canonical","extraction_status":"ok","title":"Colonic mucosal gene expression profile associated with neoplastic progression in longstanding ulcerative colitis","summary":"Introduction: Many gene expression studies of colitis-associated colorectal cancer (CA-CRC) in patients with ulcerative colitis (UC) have focused on identification of molecular drivers of progression of UC to CA- CRC. However, they have primarily studied cancerous mucosal biopsies, an approach which primarily may identify the characteristics of the established cancer mucosa and not the early molecular events driving the progression. Long-standing mucosal inflammation is suspected to be one of the main drivers of CA-CRC. Still, not all patients with UC progress and develop cancer. We hypothesise that patients with UC, who have progressed to neoplasia (progressors), have a different molecular profile of inflammation than non-progressors. Methods: We performed transcriptome profiling on 143 mucosal biopsies from non-neoplastic colonic segments of 14 UC progressors and 30 UC non-progressors. In addition, we performed profiling of lymphocyte infiltration to the mucosa of biopsies taken adjacent to biopsies used for transcriptomic analysis. Results: We found a characteristic gene expression profile for inflamed mucosa of UC progressors, which primarily is associated with progression of UC to dysplasia or cancer as opposed to long duration of disease. The gene expression profile suggests that the inflamed tissue of UC progressors is negatively enriched for biological processes such as adaptive immune responses and complement system activity and positively enriched for biological processes related to detoxification. Moreover, we found that the microenvironment in the inflamed mucosa of progressors differs from non-progressors by having fewer infiltrating B cells and less lymphoid aggregates. Conclusions: We found that inflammation of UC patients, who have progressed to dysplasia or cancer, has a different gene expression profile than that of UC non-progressors. Importantly, this profile was primarily associated with progression of disease as opposed to duration of disease. The inflamed mucosa of UC progressors may have lower levels of lymphoid organ-initiating and immune cell- attracting signals and fewer immune cells infiltrating the mucosa. Consequently, progressors may lack the ability to mount sufficient adaptive immune responses necessary to counteract driving forces of malignant transformation in UC.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":143,"included_by_policy_rows":31,"raw_sample_rows":143,"default_region_counts_json":"[{\"accession\": \"GSE236055\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"13\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"9\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"10\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"6\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"41\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"3\"}]","decision":"baseline_ok","source_date":"2025-10-20","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE24287","agent_decision":"include_canonical","extraction_status":"ok","title":"Differential early pathogenic changes in human ileal gene expression in Crohn's disease and ulcerative colitis","summary":"The aim of this study is to identify early pathogenic changes in ileal gene expression that precede the development of macroscopic disease in inflammatory bowel diseases (IBDs). We focused on two IBD phenotypes that were unlikely to overlap: 1) ileal Crohn’s disease (CD) patients undergoing initial ileocolic resection of diseased ileum; and 2) ulcerative colitis (UC) patients undergoing total colectomy. The Control patients were those patients without IBD undergoing initial right hemicolectomy or total colectomy.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":99,"included_by_policy_rows":25,"raw_sample_rows":99,"default_region_counts_json":"[{\"accession\": \"GSE24287\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"25\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"25\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2010-09-26","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE245890","agent_decision":"include_canonical","extraction_status":"ok","title":"Analysis of rectal transcriptome in ulcerative colitis (UC) patients who received tofacitinib","summary":"The gold of this study is to identify genes that differentially expressed in rectum of ulcerative colitis patients who are responisve to tofacitinib compared with the patients who are refractory to the drug. This study may help to identify preditive markers to determine tofacitinib responders prior to the treatment.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":102,"included_by_policy_rows":0,"raw_sample_rows":102,"default_region_counts_json":"[{\"accession\": \"GSE245890\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"102\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"102\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2024-10-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE261086","agent_decision":"include_canonical","extraction_status":"ok","title":"Multi-Omics Characterization of Colon Mucosa and Submucosa/Wall from Crohn's Disease Patients","summary":"Crohn’s disease (CD) is a subtype of inflammatory bowel disease (IBD) characterized by transmural disease. The concept of transmural healing (TH) has been proposed as an indicator of deep clinical remission of CD and as a predictor of favorable treatment endpoints. Understanding the pathophysiology involved in transmural disease is critical to achieving these endpoints. However, most studies have focused on the intestinal mucosa, overlooking the contribution of the intestinal wall in Crohn’s disease. Multi-omics approaches have provided new avenues for exploring the pathogenesis of Crohn’s disease and identifying potential biomarkers. . We aimed to use transcriptomic and proteomic technologies to compare immune and mesenchymal cell profiles and pathways in the mucosal and submucosa/wall compartments to better understand chronic refractory disease elements to achieve transmural healing. The results revealed similarities and differences in gene and protein expression profiles, metabolic mechanisms, and immune and non-immune pathways between these two compartments. Additionally, the identification of protein isoforms highlights the complex molecular mechanisms underlying this disease, such as decreased RTN4 isoforms (RTN4B2 and RTN4C) in the submucosa/wall which may be related to the dysregulation of enteric neural processes. These findings have the potential to inform the development of novel therapeutic strategies to achieve TH","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":52,"included_by_policy_rows":0,"raw_sample_rows":52,"default_region_counts_json":"[{\"accession\": \"GSE261086\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"17\", \"other_control\": \"17\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"17\", \"total_control\": \"17\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2024-03-15","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE264073","agent_decision":"include_canonical","extraction_status":"ok","title":"Ileal Enterocyte Brush Border Abnormalities Associate with Progressive Disease Course in Pediatric Crohn’s Disease","summary":"Objective: There is a critical need for biomarkers to predict prognosis and guide clinical care in pediatric Crohn’s disease (CD). Our previous studies of adult CD indicated ileal microvillus length as a potential prognostic biomarker for therapy response. Here, we tested if short microvillus length predicted progression of disease behavior or bowel resection surgery in pediatric CD. Design: We obtained H&E-stained ileal histology samples from 3 pediatric CD cohorts. Average microvillus length was determined for 59 Control and 377 CD samples and tested for associations with patient demographic and clinical data, RNA-seq molecular profiles, histological inflammation scores, and clinical outcomes. Results: Relative to Controls, the average microvillus length was shorter in CD samples collected at diagnostic or follow-up colonoscopy procedures. Microvillus length was generally not associated with demographic data or clinical activity indices. The CD molecular signature was functionally enriched for transporter activity and brush border membrane among the genes positively associated with microvillus length and for extracellular matrix, inflamed macrophages, and fibroblasts among the genes negatively associated with microvillus length. Microvillus length negatively correlated with histologic inflammation score, but short microvillus length phenotype could cooccur with low histologic inflammation. There was a higher likelihood of stricturing disease behavior or bowel resection surgery, but not fistulizing disease behavior, in follow-up CD samples with short microvillus length. Conclusion: Short microvillus length can predict the development of stricturing disease behavior and bowel resection surgery in pediatric CD, further supporting the potential use of this histological phenotype as a biomarker for CD prognosis.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":304,"included_by_policy_rows":304,"raw_sample_rows":304,"default_region_counts_json":"[{\"accession\": \"GSE264073\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"276\", \"ileum_control\": \"28\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"276\", \"total_control\": \"28\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2025-12-17","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE266546","agent_decision":"include_canonical","extraction_status":"ok","title":"Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's Disease","summary":"Crohn’s disease (CD) is a complex chronic inflammatory disorder with both gastrointestinal and extra-intestinal manifestations associated immune dysregulation. Analyzing 202,359 cells from 170 specimens across 83 patients, we identified a distinct epithelial cell type in both terminal ileum and ascending colon (termed “LND”) with high expression of LCN2, NOS2, and DUOX2 and genes related to antimicrobial response and immunoregulation. LND cells, confirmed by in-situ RNA and protein imaging, were rare in non-IBD controls but significantly expanded in active CD. These cells actively interacted with immune cells and specifically expressed IBD/CD susceptibility genes, as demonstrated by multimodal data, suggesting a possible role in CD immunopathogenesis. Furthermore, we discovered early and late LND subpopulations with different origins and developmental potential. A higher ratio of late to early LND cells correlated with better response to anti-TNF treatment. These findings suggest a potential pathogenic role for LND cells in both Crohn’s ileitis and colitis.","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":170,"included_by_policy_rows":102,"raw_sample_rows":170,"default_region_counts_json":"[{\"accession\": \"GSE266546\", \"ascending_cd\": \"33\", \"ascending_control\": \"24\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"25\", \"ileum_control\": \"20\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"58\", \"total_control\": \"44\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2024-07-29","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE266616","agent_decision":"include_canonical","extraction_status":"ok","title":"Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments","summary":"Crohn’s disease (CD) is a major subtype of life-long Inflammatory Bowel Disease (IBD) affecting a growing population in United States. To advance the knowledge in pathology, our study investigates into the common inflammatory feature in CD across different inflammation statuses by single-cell transcriptomics. First, we provided a detailed mucosal cellular landscape of terminal ileum (TI) and ascending colon (AC), with endoscopic diagnosis (CD inflamed, adjacent-to-inflamed, non-inflamed and non-IBD control), including a cohort of patients undergoing biological treatments. Differences between regions (TI and AC), and features of mucosal inflammation status in cellular composition are captured within the cellular landscapes. Second, we identified an inflammation cascade that include follicle-associated enterocytes and macrophages via molecules like CCL20 and S100As, as key mediators of CD inflammation. These key mediators serve as hubs in imputed cell-cell interactions under CD inflammation, expanding the interplay network with increasing disease severity. Finally, we demonstrate a scoring method by surveying the mucosa, using GWAS loci, and transcriptome features including differentially expressed genes (DEGs), and genes from a novel singular value decomposition (SVD)-based co-expression network analysis framework. Applying independently to the epithelial and immune lineage, we identify inflammation signatures that reflect disease severity. Furthermore, we report a short, robust list of epithelial and immune transcript makers whose expressions harmonize with endoscopic diagnosis and histological assessment. These markers are merely within known IBD GWAS loci. Collectively, this study narrates a shared inflammation pattern involving cells and cytokines for active CD and present a short list of markers for metrical inflammation assessment.","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":85,"included_by_policy_rows":85,"raw_sample_rows":85,"default_region_counts_json":"[{\"accession\": \"GSE266616\", \"ascending_cd\": \"20\", \"ascending_control\": \"17\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"32\", \"ileum_control\": \"16\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"52\", \"total_control\": \"33\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2024-12-16","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE270663","agent_decision":"include_canonical","extraction_status":"ok","title":"Characterisation of the regulatory landscape in Crohn’s disease reveals miRNA-associated alterations that shape anti-TNF response","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":119,"included_by_policy_rows":119,"raw_sample_rows":238,"default_region_counts_json":"[{\"accession\": \"GSE270663\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"40\", \"descending_control\": \"20\", \"descending_uc\": \"0\", \"ileum_cd\": \"39\", \"ileum_control\": \"20\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"79\", \"total_control\": \"40\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2025-07-16","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE279302","agent_decision":"include_canonical","extraction_status":"ok","title":"eQTL in diseased colon tissue identifies novel target genes associated with IBD","summary":"Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":191,"included_by_policy_rows":0,"raw_sample_rows":191,"default_region_counts_json":"[]","decision":"baseline_ok","source_date":"2024-10-16","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE282122","agent_decision":"include_canonical","extraction_status":"ok","title":"A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease","summary":"Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following adalimumab, an anti-tumour necrosis factor (anti-TNF) treatment. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies (41 subjects), revealing disease-specific differences. A systems biology-spatial analysis identified granuloma signatures in CD and interferon (IFN)-response signatures localising to T cell aggregates and epithelial damage in CD and UC. Pretreatment differences in epithelial and myeloid compartments were associated with remission outcomes in both diseases. Longitudinal comparisons demonstrated disease progression in nonremission: myeloid and T cell perturbations in CD and increased multi-cellular IFN signalling in UC. IFN signalling was also observed in rheumatoid arthritis (RA) synovium with a lymphoid pathotype. Our therapeutic atlas represents the largest cellular census of perturbation with the most common biologic treatment, anti-TNF, across multiple inflammatory diseases.","study_type_class":"target_spatial_transcriptomics","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":216,"included_by_policy_rows":81,"raw_sample_rows":216,"default_region_counts_json":"[{\"accession\": \"GSE282122\", \"ascending_cd\": \"8\", \"ascending_control\": \"3\", \"ascending_uc\": \"5\", \"descending_cd\": \"8\", \"descending_control\": \"3\", \"descending_uc\": \"19\", \"ileum_cd\": \"17\", \"ileum_control\": \"3\", \"ileum_uc\": \"0\", \"other_cd\": \"3\", \"other_control\": \"3\", \"other_uc\": \"29\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"15\", \"total_cd\": \"36\", \"total_control\": \"12\", \"total_uc\": \"68\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2024-11-19","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE284232","agent_decision":"include_canonical","extraction_status":"ok","title":"Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":73,"included_by_policy_rows":0,"raw_sample_rows":113,"default_region_counts_json":"[{\"accession\": \"GSE284232\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"62\", \"other_control\": \"4\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"62\", \"total_control\": \"4\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2025-09-30","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE290695","agent_decision":"include_canonical","extraction_status":"ok","title":"Identification of Crohn’s disease subtypes in single cell RNA sequencing signatures of treatment naïve samples across the gastrointestinal tract","summary":"Crohn’s disease (CD) is characterized by chronic inflammation throughout the intestines. Previous single cell transcriptomic studies investigated the effect of CD post therapeutic intervention, however, the extent to which therapy modifies the intestinal inflammatory environment remains to be elucidated. To this end, a treatment naïve pediatric CD cohort was recruited to investigate initial disease onset across the intestines, highlighting shared and tissue-specific consequences of disease. Ileum, colon, and rectum biopsies were obtained, and single cell RNA-sequencing was performed. A clustering stability assessment workflow was developed to ensure clustering and downstream results were robust. Tensor decomposition was utilized to identify clinically meaningful groups within the intestines. Other bioinformatic tools were utilized to investigate differences across group status within each tissue. Expected cell types were identified after the clustering stability assessment was performed. Inflammation did not strongly influence cellular proportion profiles due to heterogeneity across donor and tissue. Tensor decomposition revealed distinct mesenchymal and cytotoxic T cell-mediated sources of disease pathology, corresponding to previously identified fibrotic and pro-inflammatory disease progression. Integrating transcriptomics and genome wide association summary statistics for CD suggested myeloid cells and T cells drive disease, highlighting potential cellular therapeutic targets. Tensor decomposition stratified donors into clinically meaningful groups based on their transcriptomic profile, suggesting these signatures can be utilized for personalized medicine.","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":190,"included_by_policy_rows":76,"raw_sample_rows":190,"default_region_counts_json":"[{\"accession\": \"GSE290695\", \"ascending_cd\": \"14\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"2\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"54\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"114\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"2\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"190\", \"total_control\": \"0\", \"total_uc\": \"0\", \"transverse_cd\": \"4\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2025-04-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE304649","agent_decision":"include_canonical","extraction_status":"ok","title":"Myeloid Cell Adhesion Molecule 1 (CADM1) promotes pro-inflammatory signaling in human Inflammatory Bowel Diseases","summary":"Cytotoxic T cells have been postulated to facilitate the destruction of intestinal epithelium in inflammatory bowel diseases (IBDs). CADM1, which encodes a membrane adhesion protein that can bind the T cell receptor CRTAM, was markedly up regulated in colon of IBD patients compared to non-IBD (NIBD) patients. We then identified CADM1 enrichment in multiple immune cell clusters including macrophages and dendritic cells in the colons of IBD patients. Increased numbers of CADM1+ myeloid cells were measured adjacent to CD8+ T cells within colons of ulcerative colitis patients compared to NIBD patients. Conditional deletion of Cadm1 in myeloid cells resulted in reduced numbers of activated T cell populations and protected mice from chemical-induced colitis. Similarly, administration of a Cadm1 ‘neutralizing’ antibody which binds its extracellular domain reduced tissue inflammation and breakdown of the intestinal epithelium and crypts after induction of colitis in mice. Lastly, serum levels of sCADM1 were elevated in IBD patients compared to NIBD controls and treatment of LPMCs with recombinant sCADM1 enhanced inflammatory STAT3 phosphorylation. Therefore, we concluded that CADM1 is a mediator of pro-inflammatory signaling cascades in the colon and a potential therapeutic target for the IBDs.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":59,"included_by_policy_rows":19,"raw_sample_rows":59,"default_region_counts_json":"[{\"accession\": \"GSE304649\", \"ascending_cd\": \"0\", \"ascending_control\": \"6\", \"ascending_uc\": \"4\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"2\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"10\", \"other_uc\": \"30\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"5\", \"total_cd\": \"0\", \"total_control\": \"16\", \"total_uc\": \"43\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"2\"}]","decision":"baseline_ok","source_date":"2025-10-11","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE317503","agent_decision":"include_canonical","extraction_status":"ok","title":"Reference-guided genome assembly of long non-coding RNA transcripts reveals target genes associated with Crohn’s disease","summary":"RNA-seq of colon tissue from CD patients and non-IBD controls","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":140,"included_by_policy_rows":0,"raw_sample_rows":140,"default_region_counts_json":"[{\"accession\": \"GSE317503\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"50\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"50\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2026-02-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE3629","agent_decision":"include_canonical","extraction_status":"ok","title":"Molecular Marker for predicting development of cancer in ulcerative colitis","summary":"Samples were taken from either surgically resected specimens or during surveillance colonoscopic examination. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting development of cancer and/or dysplasia in ulcerative colitis, and to characterize potential diagnostic markers in UC-associated neoplasm. Keywords: repeat","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":121,"included_by_policy_rows":0,"raw_sample_rows":121,"default_region_counts_json":"[{\"accession\": \"GSE3629\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"53\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"53\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2007-02-28","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE4183","agent_decision":"include_canonical","extraction_status":"ok","title":"Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature","summary":"Background and Aims: Gene expression analysis of colon biopsies using high-density oligonucleotide microarray can contribute to the understanding of local pathophysiological alterations and to functional classification of precancerous adenoma, different stage colorectal carcinomas (CRC) and inflammatory bowel diseases (IBD). Results: Significant overexpression of collagen IV, lipocalin-2, caveolin-1, calumenin genes, and significant dowregulation of aquaporin-8, amnionless homolog, prostaglandin D2 receptor genes were detected in CRC patients compared to normal. Adenoma samples were characterized by upregulated CD44 antigen, met proto-oncogene and downregulated chemokine ligand-12, ADAM-like decysin-1 and ATP-binding casette A8 discriminatory genes. In IBD samples significantly increased lipocalin-2, interferon induced transmembrane protein 1 and 3 mRNA levels, decreased zinc finger protein 91 and transient receptor potential cation channel M6 mRNA levels were found. Ulcerative colitis and Crohn’s disease can be distinguished according to the top five genes: cyclin-G2; tripartite motif-containing-31; TNFR shedding aminopeptidase regulator-1; C-type lectin superfamily member-14 and AMICA. 88.3-97.8% of the cases was correctly classified according to discriminatory genes. Conclusions: Our whole genomic microarray analysis of biopsy samples provides discriminative signatures, and an insight into pathophysiological background of colonic diseases. The results afford a data warehouse which can be further mined for in-depth pathway analyses. Keywords: Colon biopsy specimens in diseased and normal state","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":106,"included_by_policy_rows":0,"raw_sample_rows":106,"default_region_counts_json":"[{\"accession\": \"GSE4183\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"16\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"16\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2007-10-31","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE47908","agent_decision":"include_canonical","extraction_status":"ok","title":"Transcriptional analysis of left-sided colitis, pancolitis and ulcerative colitis-associated dysplasia","summary":"This study characterizes the inflammatory processes in left-sided colitis, pancolitis, and UC-associated dysplasia at the transcriptional level in colonics biopsies in order to identify potential biomarkers and transcripts of importance for the carcinogenic behaviour of chronic inflammation","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":120,"included_by_policy_rows":120,"raw_sample_rows":120,"default_region_counts_json":"[{\"accession\": \"GSE47908\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"30\", \"descending_uc\": \"90\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"30\", \"total_uc\": \"90\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2014-12-31","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE48634","agent_decision":"include_canonical","extraction_status":"ok","title":"Mucosal transcriptomics implicates under expression of FAM5C in the pathogenesis of ulcerative colitis","summary":"Background and aims: Mucosal abnormalities are potentially important in the primary pathogenesis of ulcerative colitis (UC). We investigated the mucosal transcriptomic expression profiles of biopsies from patients with UC and healthy controls (HC), taken from macroscopically non-inflamed tissue from the terminal ileum and three colonic locations with the objective of identifying abnormal molecules that might be involved in disease development. Methods: Whole-genome transcriptional analysis was performed on intestinal biopsies taken from 24 UC, 26 HC and 14 patients with Crohn’s disease. Differential gene expression analysis was performed at each tissue location separately and results were then meta-analysed using Fisher’s method. Significantly differentially expressed genes were validated using qPCR. Gene location within the colon was determined using immunohistochemistry, subcellular fractionation, electron and confocal microscopy. DNA methylation was quantified by pyrosequencing. Results: Seven probes were abnormally expressed throughout the colon in UC patients with Family with sequence similarity member 5 C (FAM5C) being the most significantly underexpressed. Attenuated expression of FAM5C in UC was independent of inflammation, unrelated to phenotype or treatment, and remained low at rebiopsy approximately 23 months later. FAM5C is localised to the brush border of the colonic epithelium and expression is influenced by DNA methylation within its promoter. Conclusion: Genome-wide expression analysis of non-inflamed mucosal biopsies from UC patients identified FAM5C as significantly under-expressed throughout the colon in a major sub-set of patients with UC. Low levels of this gene could predispose to or contribute to the maintenance of the characteristic mucosal inflammation seen in this condition.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":171,"included_by_policy_rows":112,"raw_sample_rows":171,"default_region_counts_json":"[{\"accession\": \"GSE48634\", \"ascending_cd\": \"7\", \"ascending_control\": \"13\", \"ascending_uc\": \"16\", \"descending_cd\": \"9\", \"descending_control\": \"17\", \"descending_uc\": \"20\", \"ileum_cd\": \"5\", \"ileum_control\": \"13\", \"ileum_uc\": \"12\", \"other_cd\": \"13\", \"other_control\": \"26\", \"other_uc\": \"20\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"34\", \"total_control\": \"69\", \"total_uc\": \"68\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2014-09-05","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE50594","agent_decision":"include_canonical","extraction_status":"ok","title":"EFFECT OF A NOVEL PROBIOTIC PREPARATION ON INDUCTION AND MAINTENANCE OF REMISSION IN ULCERATIVE COLITIS PATIENTS: A DOUBLE-BLIND PLACEBO CONTROLLED TRIAL","summary":"This study investigated the effect of a novel probiotic preparation on the colonic mucosal gene expression in UC patients, using whole genome gene expression microarrays.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":54,"included_by_policy_rows":0,"raw_sample_rows":54,"default_region_counts_json":"[{\"accession\": \"GSE50594\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"21\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"21\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2016-05-24","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE51785","agent_decision":"include_canonical","extraction_status":"ok","title":"Molecular patterns in human ulcerative colitis and correlation with response to infliximab","summary":"Background & Aims. As a T cell-mediated disease of the colonic epithelium, ulcerative colitis (UC) is likely to share pathogenic elements with other T cell-mediated inflammatory diseases. Recently we showed T cell-mediated rejection of kidney and heart transplants share large scale molecular changes. We hypothesized that UC would manifest a similar disturbance, and that these features would correlate with response to infliximab. Results. UC biopsies manifested coordinate transcript changes resembling rejecting transplants, with T cell, IFNG-induced, macrophage, and injury transcripts increasing while parenchymal transcripts decreased. The disturbance expressed as principal component 1 correlated with conventional assessments e.g. Mayo scores, serum albumin, and lymphoplasmacytic infiltrate. When assessed in published microarray studies, the disturbance predicted response to infliximab: patients with intense disturbance did not achieve clinical response, although quantitative improvement was usually seen even in non-responders. Similar changes were seen in Crohn’s colitis (CDc). Conclusions. The molecular phenotype of UC manifests a large scale coordinate disturbance reflecting changes in inflammatory cells and parenchymal elements that correlates with conventional features and predicts response to infliximab.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":56,"included_by_policy_rows":0,"raw_sample_rows":56,"default_region_counts_json":"[{\"accession\": \"GSE51785\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"43\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"43\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2014-12-22","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE57945","agent_decision":"include_canonical","extraction_status":"ok","title":"Core Ileal Transcriptome in Pediatric Crohn Disease","summary":"We report the global pattern of ileal gene expression in a cohort of 359 treatment-naïve pediatric Crohn Disease, Ulcerative Colitis patients and controls. We focus on genes with consistent altered expression in inflamed and unaffected ileum of CD [ileal-involved CD (iCD) and non-invloved ileal CD (cCD)], but not in the ileum of ulcerative colitis or control.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":322,"included_by_policy_rows":233,"raw_sample_rows":322,"default_region_counts_json":"[{\"accession\": \"GSE57945\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"191\", \"ileum_control\": \"42\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"191\", \"total_control\": \"42\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2014-07-24","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE59071","agent_decision":"include_canonical","extraction_status":"ok","title":"Mucosal gene expression profiling in patients with inflammatory bowel disease","summary":"Microarrays were used to analyze the gene expression in endoscopic-derived intestinal mucosal biopsies from patients with inflammatory bowel disease (IBD) and controls","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":116,"included_by_policy_rows":0,"raw_sample_rows":116,"default_region_counts_json":"[{\"accession\": \"GSE59071\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"8\", \"other_control\": \"11\", \"other_uc\": \"74\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"8\", \"total_control\": \"11\", \"total_uc\": \"74\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2015-05-27","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE62207","agent_decision":"include_canonical","extraction_status":"ok","title":"Ileal immune maturation in Pediatric Crohn's Disease","summary":"We report the global pattern of ileal gene expression in a cohort of 310 treatment-naïve pediatric Crohn Disease patients and controls. We focus on genes with consistent altered expression in the ileum of younger (Paris age A1a) vs older (Paris age A1b) patients.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":310,"included_by_policy_rows":310,"raw_sample_rows":310,"default_region_counts_json":"[{\"accession\": \"GSE62207\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"259\", \"ileum_control\": \"51\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"259\", \"total_control\": \"51\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2015-10-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE66407","agent_decision":"include_canonical","extraction_status":"ok","title":"Gut biopsies from patients with Crohn's Disease and Ulcerative Colitis and healthy controls","summary":"For IBD, >163 susceptibility loci have been revealed by Genome-wide association studies (GWAS). Still only 13.6% of the heritability in CD and 7.5% in UC can be explained by the loci that have been revealed (23128233). In an endeavor to pinpoint additional IBD genes and pathways involved in the disease, we have made a large scale transcriptome analysis of human pince 380 biopsies from 109 donors. We identified novel genes and protein-protein interaction networks that are strongly associated with disease and gives new insight to the pathology of both CD and UC and the resulting inflammation","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":363,"included_by_policy_rows":136,"raw_sample_rows":368,"default_region_counts_json":"[{\"accession\": \"GSE66407\", \"ascending_cd\": \"2\", \"ascending_control\": \"14\", \"ascending_uc\": \"2\", \"descending_cd\": \"8\", \"descending_control\": \"14\", \"descending_uc\": \"4\", \"ileum_cd\": \"12\", \"ileum_control\": \"6\", \"ileum_uc\": \"0\", \"other_cd\": \"8\", \"other_control\": \"38\", \"other_uc\": \"26\", \"sigmoid_cd\": \"10\", \"sigmoid_control\": \"14\", \"sigmoid_uc\": \"24\", \"total_cd\": \"47\", \"total_control\": \"99\", \"total_uc\": \"62\", \"transverse_cd\": \"7\", \"transverse_control\": \"13\", \"transverse_uc\": \"6\"}]","decision":"baseline_ok","source_date":"2022-09-07","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE67106","agent_decision":"include_canonical","extraction_status":"ok","title":"Transcriptomic landscape of lncRNAs in Inflammatory Bowel Disease","summary":"Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn’s disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD. In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in inflamed and non-inflamed colon pinch biopsies from the IBD patients using expression microarrays platform. In this study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC compared to the healthy controls. In case of inflamed CD and UC (iCD and iUC), we identified 438 and 745 differentially expressed lncRNAs, respectively, while in case of the non-inflamed CD and UC (niCD and niUC), we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (p-value < 0.001, Pearson’s Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed that they are involved in immune response, pro-inflammatory cytokine activity and MHC protein complex. The lncRNA expression profiling in both inflamed and non-inflamed CD and UC, successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggests their potential as biomarkers in IBD.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":192,"included_by_policy_rows":84,"raw_sample_rows":192,"default_region_counts_json":"[{\"accession\": \"GSE67106\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"6\", \"descending_control\": \"8\", \"descending_uc\": \"0\", \"ileum_cd\": \"10\", \"ileum_control\": \"4\", \"ileum_uc\": \"0\", \"other_cd\": \"4\", \"other_control\": \"16\", \"other_uc\": \"12\", \"sigmoid_cd\": \"12\", \"sigmoid_control\": \"8\", \"sigmoid_uc\": \"18\", \"total_cd\": \"42\", \"total_control\": \"44\", \"total_uc\": \"30\", \"transverse_cd\": \"10\", \"transverse_control\": \"8\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2015-04-10","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE72221","agent_decision":"include_canonical","extraction_status":"ok","title":"Characterization of LncRNA BC012900 among long non-coding RNAs differentially expressed in ulcerative colitis","summary":"In this report, we provide a comprehensive assessment of the expression of ~17000 lncRNAs on 60 colonic samplesin colon tissues from patients with IBD, irritable bowel syndrome, infectious colitis and healthy controls. We also explored the possibility of using cRNAs as biomarkers distinguish active UC from normal. To investigate the mechanism offunctional role these IBD-associated lncRNAs in the development of IBD, we then focused on a ncRNA highlyexpressed in the UC-associated lncRNAactive UC, BC012900. We , to characterized its cellular localization, expression regulation and biological function. We . We found that BC012900 and its adjacent gene, dual specificity phosphatase 4 (DUSP4) are functionally distinct, with BC012900 modulating. Overexpression of BC012900 resulted in usceptibility to apoptosis. Our study provides the first evidence that lncRNAs may play potential roles in development and persistence of active UC.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":57,"included_by_policy_rows":34,"raw_sample_rows":57,"default_region_counts_json":"[{\"accession\": \"GSE72221\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"5\", \"sigmoid_control\": \"14\", \"sigmoid_uc\": \"15\", \"total_cd\": \"5\", \"total_control\": \"14\", \"total_uc\": \"15\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2016-01-28","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE72819","agent_decision":"include_canonical","extraction_status":"ok","title":"Gene expression of baseline biopsies from etrolizumab-treated ulcerative colitis (UC) patients","summary":"RNA sequencing was performed on RNA isolated from baseline biopsies from UC patients enrolled in the Phase II EUCALYPTUS study of etrolizumab. Gene expression differences were identified in a subset of anti-TNF naïve patients that achieved clinical remission at 10 weeks in response to etrolizumab.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":73,"included_by_policy_rows":0,"raw_sample_rows":73,"default_region_counts_json":"[{\"accession\": \"GSE72819\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"73\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"73\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2015-10-26","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE73094","agent_decision":"include_canonical","extraction_status":"ok","title":"Genes in Inflammatory Bowel Disease-Associated Risk Loci Demonstrate Genotype-, Tissue-, and Inflammation-Specific Patterns of Expression in Terminal Ileum and Colon Mucosal Tissue","summary":"With a greater understanding of the genetic risk variants associated with inflammatory bowel disease, there is a need to prioritize candidate genes within risk loci leading to the disease-SNP association. We created a custom NanoString probeset to capture 678 genes of interest in IBD (including 440 genes encoded within IBD risk loci and 15 housekeeping genes) - 22% of genes were not captured on traditional microarray platforms. Total RNA extracted from terminal ileum and colon tissues (uninflamed and inflamed) was used from patients with Crohn's disease and ulcerative colitis and healthy controls. We studied differential expression and performed an eQTL analysis to prioritize candidate genes within the risk loci.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":989,"included_by_policy_rows":299,"raw_sample_rows":989,"default_region_counts_json":"[{\"accession\": \"GSE73094\", \"ascending_cd\": \"5\", \"ascending_control\": \"11\", \"ascending_uc\": \"5\", \"descending_cd\": \"10\", \"descending_control\": \"11\", \"descending_uc\": \"15\", \"ileum_cd\": \"159\", \"ileum_control\": \"13\", \"ileum_uc\": \"2\", \"other_cd\": \"50\", \"other_control\": \"4\", \"other_uc\": \"56\", \"sigmoid_cd\": \"23\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"41\", \"total_cd\": \"247\", \"total_control\": \"39\", \"total_uc\": \"123\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"4\"}]","decision":"baseline_ok","source_date":"2016-08-10","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE73661","agent_decision":"include_canonical","extraction_status":"ok","title":"The effect of vedolizumab (anti-α4β7-integrin) therapy on colonic mucosal gene expression in patients with ulcerative colitis (UC)","summary":"Microarrays were used to investigate the the effect of vedolizumab (VDZ) therapy on colonic mucosal gene expression in UC patients and compared the changes to those observed with infliximab (IFX) therapy.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":178,"included_by_policy_rows":0,"raw_sample_rows":178,"default_region_counts_json":"[{\"accession\": \"GSE73661\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"12\", \"other_uc\": \"67\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"12\", \"total_uc\": \"67\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2016-10-11","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE75214","agent_decision":"include_canonical","extraction_status":"ok","title":"Mucosal gene expression profiling in patients with inflammatory bowel disease study","summary":"Microarrays were used to analyze the gene expression in endoscopic-derived intestinal mucosal biopsies from patients with inflammatory bowel diseas (IBD) and controls","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":194,"included_by_policy_rows":62,"raw_sample_rows":194,"default_region_counts_json":"[{\"accession\": \"GSE75214\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"51\", \"ileum_control\": \"11\", \"ileum_uc\": \"0\", \"other_cd\": \"8\", \"other_control\": \"11\", \"other_uc\": \"74\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"59\", \"total_control\": \"22\", \"total_uc\": \"74\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2017-09-14","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE81266","agent_decision":"include_canonical","extraction_status":"ok","title":"Ileal pouch transcriptomics reveal shared pathogenesis between pouchitis and ulcerative colitis","summary":"UC pouchitis is a potential model of UC. We prospectively examined the pouch transcriptomes of UC and familial adenomatous polyposis (FAP) IPAA patients to unveil molecular mechanisms of UC pouchitis susceptibility. Methods: Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7. RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit. Results: Unlike FAP patients, UC subjects exhibited a large set of differentially expressed genes (DEGs) between pouch and pre-pouch mucosa as early as 4 months after pouch functionalization. Functional pathway analysis of DEGs in UC pouch revealed: (1) Gain of colon-associated gene expressions and loss of ileum associated gene expressions, (2) enhanced state of immune/inflammatory response, and (3) suppressed xenobiotic, lipid, and bile acid metabolic pathways. These changes were corroborated upon reanalysis of a published larger cross-sectional study of UC and FAP patients. Moreover, >70% of DEGs mapped to published IBD and normal colonic microarray datasets displayed directional changes consistent with active UC, but not Crohn's disease. Conclusions: UC patients exhibit a unique transcriptomic response to ileal pouch creation that can be observed well before disease. The transcriptome alterations provide insights into pouchitis","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":154,"included_by_policy_rows":4,"raw_sample_rows":154,"default_region_counts_json":"[{\"accession\": \"GSE81266\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"4\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"142\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"4\", \"total_uc\": \"142\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2016-05-11","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE83448","agent_decision":"include_canonical","extraction_status":"ok","title":"Genome-wide transcriptional analysis in intestinal biopsies from Crohn's disease (CD) patients.","summary":"Differential gene expression analysis between CD patients and controls to identify the transcriptional signature that defines the inflamed intestinal mucosa in CD.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":53,"included_by_policy_rows":0,"raw_sample_rows":53,"default_region_counts_json":"[{\"accession\": \"GSE83448\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"19\", \"other_control\": \"14\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"19\", \"total_control\": \"14\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2020-06-08","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE83687","agent_decision":"include_canonical","extraction_status":"ok","title":"A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease","summary":"This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":134,"included_by_policy_rows":41,"raw_sample_rows":134,"default_region_counts_json":"[{\"accession\": \"GSE83687\", \"ascending_cd\": \"1\", \"ascending_control\": \"17\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"5\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"2\", \"ileum_uc\": \"1\", \"other_cd\": \"0\", \"other_control\": \"21\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"11\", \"sigmoid_uc\": \"0\", \"total_cd\": \"1\", \"total_control\": \"60\", \"total_uc\": \"1\", \"transverse_cd\": \"0\", \"transverse_control\": \"4\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2017-07-07","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE87473","agent_decision":"include_canonical","extraction_status":"ok","title":"Gene expression profiling of mucosal biopsies from pediatric or adult patients with moderately to severely active ulcerative colitis","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":127,"included_by_policy_rows":0,"raw_sample_rows":127,"default_region_counts_json":"[{\"accession\": \"GSE87473\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"21\", \"other_uc\": \"106\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"21\", \"total_uc\": \"106\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2018-12-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE92415","agent_decision":"include_canonical","extraction_status":"ok","title":"Characterization of molecular response to Golimumab in Ulcerative Colitis by mucosal biopsy mRNA expression profiling: results from PURSUIT-SC induction study","summary":"To evaluate the effects of induction treatment with an anti-TNF, golimumab (GLM), on gene expression in patients with moderately to severely active ulcerative colitis (UC), we performed mRNA microarray studies on colon biopsies from patients who participated in the PURSUIT-SC induction study and additional samples from 21 healthy subjects. Comparisons were conducted between baseline UC (n=87) and healthy (n=21), and week 6 (n=75) vs. baseline (n=87) prior to treatment. A significant difference was observed in mRNA expression between UC and healthy. Significant expression modulations were identified in patients who responded to GLM at week 6, but not GLM-treated non-responders or placebo-treated subjects.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":183,"included_by_policy_rows":0,"raw_sample_rows":183,"default_region_counts_json":"[{\"accession\": \"GSE92415\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"21\", \"other_uc\": \"162\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"21\", \"total_uc\": \"162\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2018-12-03","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE93624","agent_decision":"include_canonical","extraction_status":"ok","title":"Profiling of Ileal Transcriptome in Pediatric Crohn Disease","summary":"We report ileal gene expression at diagnosis in a cohort of 210 treatment-naïve patients of pediatric Crohn's disease and 35 non-IBD controls from the RISK study. After three years of follow-up after diagnosis, 27 of the CD patients progressed to complicated disease (B2 and/or B3). We aim to test whether Transcriptional Risk Scores helps to distinguish between patient subgroups, improving the predictive power gained from Genetic Risk Scores.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":245,"included_by_policy_rows":245,"raw_sample_rows":245,"default_region_counts_json":"[{\"accession\": \"GSE93624\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"210\", \"ileum_control\": \"35\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"210\", \"total_control\": \"35\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2017-06-20","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE95095","agent_decision":"include_canonical","extraction_status":"ok","title":"Differential Gene Expression between involved and uninvolved sites of Crohn’s disease: Insights into a Distinctive Pathogenesis Profile","summary":"Our objective was to elucidate patterns of gene expression underlying the progression of CD disease. Surgery biopsies (n=60) were assayed using the Illumina cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) microarray process specifically designed for use with Formalin-Fixed, Paraffin-Embedded (FFPE) clinical samples. Tissue was sampled in consecutive active involved and uninvolved sites at the same time in individual CD patients, and these samples (CD involved and CD uninvolved) were compared with each other as well as to non-inflammatory bowel disease (non-IBD) healthy controls.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":60,"included_by_policy_rows":0,"raw_sample_rows":60,"default_region_counts_json":"[{\"accession\": \"GSE95095\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"12\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"12\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2019-02-20","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE95437","agent_decision":"include_canonical","extraction_status":"ok","title":"The transcription start site and enhancer landscape of the descending colon in inflammatory bowel disease","summary":"Inflammatory bowel disease (IBD) is a common and chronic gut disorder, with two subtypes: Crohn's disease (CD) and ulcerative colitis (UC), which are challenging to diagnose. The molecular pathology IBD is not well understood, and the underlying gene regulatory regions have not been comprehensively investigated. Relatedly, most IBD-associated SNPs are located in non-coding regions, and may effect gene regulation. Here, we profiled genome-wide promoter and enhancer activity in the descending colon of IBD patients. IBD-induced enhancer and promoters are highly enriched for IBD-associated SNPs, and can predict IBD diagnosis with an accuracy of 85% in an external cohort.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":94,"included_by_policy_rows":74,"raw_sample_rows":94,"default_region_counts_json":"[{\"accession\": \"GSE95437\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"20\", \"descending_control\": \"29\", \"descending_uc\": \"25\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"20\", \"total_control\": \"29\", \"total_uc\": \"25\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2018-03-14","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE97012","agent_decision":"include_canonical","extraction_status":"ok","title":"Integrated Analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":68,"included_by_policy_rows":14,"raw_sample_rows":68,"default_region_counts_json":"[{\"accession\": \"GSE97012\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"2\", \"descending_cd\": \"1\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"3\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"27\", \"other_uc\": \"0\", \"sigmoid_cd\": \"3\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"4\", \"total_cd\": \"7\", \"total_control\": \"27\", \"total_uc\": \"7\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"1\"}]","decision":"baseline_ok","source_date":"2017-11-12","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE98820","agent_decision":"include_canonical","extraction_status":"ok","title":"Gene expression data from human intestinal biopsies","summary":"Anti-TNFα therapy induces mucosal healing in a large proportion of Crohn’s disease (CD) patients, but the mechanisms underlying this process are not fully elucidated. To this end we examined molecular effects of adalimumab treatment in CD. CD patients (n=10) underwent ileocolonoscopy were sampled for mucosal biopsies before and after three months of adalimumab treatment. Collected material was analyzed using transcriptome microarray analysis. All patients were responders and eight patients reached clinical remission. Mucosal transcriptome analyses demonstrated that anti-inflammatory and tissue-repair gene-sets were upregulated in inflamed mucosa, in addition to proinflammatory and tissue-destruction-related genes. After treatment, genes promoting inflammation or tissue-destruction were downregulated. , and these genes are primarily expressed in innate leukocytes and stromal cells. Expression of anti-inflammatory and tissue-repair-related genes was also downregulated, but to a lesser degree. Of note, various parts of the colon displayed distinct gene-expression profiles. Adalimumab operates by down-shifting several proinflammatory arms of both the innate and adaptive immune-system, but does not disturb regulatory T-cells. Anti-inflammatory and tissue-repair machineries are upregulated already during active inflammation, but are not effective until proinflammatory drivers have been silenced.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":160,"included_by_policy_rows":48,"raw_sample_rows":160,"default_region_counts_json":"[{\"accession\": \"GSE98820\", \"ascending_cd\": \"6\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"13\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"5\", \"other_control\": \"0\", \"other_uc\": \"0\", \"sigmoid_cd\": \"5\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"29\", \"total_control\": \"0\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2020-05-11","source_date_kind":"release_date"},{"source":"HCA","accession":"CAE461DE-ECBD-482F-A5D4-11D607FC12BA","agent_decision":"include_canonical","extraction_status":"ok","title":"The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon","summary":"Crohn's disease (CD) is a chronic gastrointestinal disease that is increasing in prevalence worldwide. CD is multifactorial, involving the complex interplay of genetic, immune, and environmental factors, necessitating a system-level understanding of its etiology. To characterize cell-type-specific transcriptional heterogeneity in active CD, we profiled 720,633 cells from the terminal ileum and colon of 71 donors with varying inflammation status. Our integrated datasets revealed organ- and compartment-specific responses to acute and chronic inflammation; most immune changes were in cell composition, whereas transcriptional changes dominated among epithelial and stromal cells. These changes correlated with endoscopic inflammation, but small and large intestines exhibited distinct responses, which were particularly apparent when focusing on IBD risk genes. Finally, we mapped markers of disease-associated myofibroblast activation and identified CHMP1A, TBX3, and RNF168 as regulators of fibrotic complications. Altogether, our results provide a roadmap for understanding cell-type- and organ-specific differences in CD and potential directions for therapeutic development.","study_type_class":"target_single_cell_rnaseq","technology_field":"HCA Azul sample index metadata","target_sample_rows":134,"included_by_policy_rows":71,"raw_sample_rows":134,"default_region_counts_json":"[{\"accession\": \"CAE461DE-ECBD-482F-A5D4-11D607FC12BA\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"57\", \"ileum_control\": \"10\", \"ileum_uc\": \"0\", \"other_cd\": \"28\", \"other_control\": \"35\", \"other_uc\": \"0\", \"sigmoid_cd\": \"4\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"89\", \"total_control\": \"45\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"baseline_ok","source_date":"2023-02-01","source_date_kind":"submission_date"},{"source":"HCA","accession":"CD61771B-661A-4E19-B269-6E5D95350DE6","agent_decision":"include_canonical","extraction_status":"ok","title":"Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.","summary":"Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC). To understand their cell type specificities and pathways of action, we generate an atlas of 366,650 cells from the colon mucosa of 18 UC patients and 12 healthy individuals, revealing 51 epithelial, stromal, and immune cell subsets, including BEST4<sup>+</sup> enterocytes, microfold-like cells, and IL13RA2<sup>+</sup>IL11<sup>+</sup> inflammatory fibroblasts, which we associate with resistance to anti-TNF treatment. Inflammatory fibroblasts, inflammatory monocytes, microfold-like cells, and T cells that co-express CD8 and IL-17 expand with disease, forming intercellular interaction hubs. Many UC risk genes are cell type specific and co-regulated within relatively few gene modules, suggesting convergence onto limited sets of cell types and pathways. Using this observation, we nominate and infer functions for specific risk genes across GWAS loci. Our work provides a framework for interrogating complex human diseases and mapping risk variants to cell types and pathways.","study_type_class":"target_single_cell_rnaseq","technology_field":"HCA Azul sample index metadata","target_sample_rows":133,"included_by_policy_rows":74,"raw_sample_rows":133,"default_region_counts_json":"[{\"accession\": \"CD61771B-661A-4E19-B269-6E5D95350DE6\", \"ascending_cd\": \"0\", \"ascending_control\": \"24\", \"ascending_uc\": \"8\", \"descending_cd\": \"0\", \"descending_control\": \"4\", \"descending_uc\": \"2\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"12\", \"other_uc\": \"47\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"20\", \"total_cd\": \"0\", \"total_control\": \"48\", \"total_uc\": \"85\", \"transverse_cd\": \"0\", \"transverse_control\": \"8\", \"transverse_uc\": 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\"ileum_control\": \"44\", \"ileum_uc\": \"0\", \"other_cd\": \"56\", \"other_control\": \"45\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"112\", \"total_control\": \"89\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"custom_override_required","source_date":"2024-03-23","source_date_kind":"first_public_date"},{"source":"GEO","accession":"GSE102133","agent_decision":"include_alias","extraction_status":"ok","title":"Mucosal gene expression profiling in ileum of patients with Crohn's disease","summary":null,"study_type_class":"target_expression_array","technology_field":null,"target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":154,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2019-03-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE107499","agent_decision":"include_alias","extraction_status":"ok","title":"Expression data from Ulcerative Colitis subjects","summary":null,"study_type_class":"target_expression_array","technology_field":null,"target_sample_rows":119,"included_by_policy_rows":47,"raw_sample_rows":119,"default_region_counts_json":"[{\"accession\": \"GSE107499\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"2\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"12\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"28\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"25\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"75\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"8\"}]","decision":"source_alias_confirmed","source_date":"2018-04-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE128435","agent_decision":"include_alias","extraction_status":"ok","title":"Differences in expression profiling between tumoral colorectal carcinomas subsets and normal tissue and polyps [mRNA]","summary":null,"study_type_class":"target_expression_array","technology_field":null,"target_sample_rows":58,"included_by_policy_rows":0,"raw_sample_rows":58,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2019-03-19","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE152316","agent_decision":"include_alias","extraction_status":"ok","title":"Etrolizumab treatment in Crohn's disease (Bergamot) cohort 1 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from patients with inflammatory bowel disease and colorectal cancer","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":95,"included_by_policy_rows":0,"raw_sample_rows":96,"default_region_counts_json":"[{\"accession\": \"GSE166925\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"19\", \"other_control\": \"42\", \"other_uc\": \"10\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"19\", \"total_control\": \"42\", \"total_uc\": \"10\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": 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\"other_uc\": \"206\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"11\", \"total_uc\": \"206\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"source_alias_confirmed","source_date":"2018-12-07","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP149847","agent_decision":"include_alias","extraction_status":"ok","title":"Differences in tissue immune cell populations following hematopoietic stem cell transplantation in Crohn's disease patients","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":80,"included_by_policy_rows":0,"raw_sample_rows":80,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2019-01-29","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP181666","agent_decision":"include_alias","extraction_status":"ok","title":"Single-Cell Analyses Elucidate the Cellular and Molecular Landscape of Ulcerative Colitis","summary":null,"study_type_class":"target_single_cell_rnaseq","technology_field":null,"target_sample_rows":41,"included_by_policy_rows":0,"raw_sample_rows":103,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2020-07-19","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP226476","agent_decision":"include_alias","extraction_status":"ok","title":"Differences in tissue populations following hematopoietic stem cell transplantation in Crohn's disease patients","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":158,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2020-10-23","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP303290","agent_decision":"include_alias","extraction_status":"ok","title":"Characterization of the IL23-IL17 immune axis in IBD patients","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":170,"included_by_policy_rows":0,"raw_sample_rows":170,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2021-11-28","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP336051","agent_decision":"include_alias","extraction_status":"ok","title":"RNA sequencing of CD11b+ cells isolated from human gut mucosal biopsies of IBD patients","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":58,"included_by_policy_rows":5,"raw_sample_rows":58,"default_region_counts_json":"[{\"accession\": \"SRP336051\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"5\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"2\", \"other_control\": \"0\", \"other_uc\": \"13\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"7\", \"total_control\": \"0\", \"total_uc\": \"13\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"source_alias_confirmed","source_date":"2022-08-25","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP338215","agent_decision":"include_alias","extraction_status":"ok","title":"Transcriptional behavior of regulatory T cells predicts IBD patient responses to vedolizumab therapy","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":172,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2022-08-25","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP343308","agent_decision":"include_alias","extraction_status":"ok","title":"RNA-seq of Korean Inflammatory Bowel Disease tissues","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":127,"included_by_policy_rows":0,"raw_sample_rows":127,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2021-12-14","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP351557","agent_decision":"include_alias","extraction_status":"ok","title":"IBD HIBEC and HILEC transcriptome compendium","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":54,"included_by_policy_rows":0,"raw_sample_rows":54,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2021-12-23","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP402091","agent_decision":"include_alias","extraction_status":"ok","title":"Regional transcriptomics and proteomics of DMPK genes in human intestine","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":61,"included_by_policy_rows":0,"raw_sample_rows":61,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2023-06-05","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP425364","agent_decision":"include_alias","extraction_status":"ok","title":"Developing biomarkers incorporating high throughput RNA, DNA, small RNA sequencing and protein expression in Inflammatory Bowel Disease using formalin-fixed, paraffin-embedded (FFPE) tissue samples","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":201,"included_by_policy_rows":100,"raw_sample_rows":201,"default_region_counts_json":"[{\"accession\": \"SRP425364\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"56\", \"ileum_control\": \"44\", \"ileum_uc\": \"0\", \"other_cd\": \"56\", \"other_control\": \"45\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"112\", \"total_control\": \"89\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"source_alias_confirmed","source_date":"2024-03-23","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP434404","agent_decision":"include_alias","extraction_status":"ok","title":"Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis [bulk RNASeq]","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":226,"included_by_policy_rows":0,"raw_sample_rows":226,"default_region_counts_json":"[{\"accession\": \"SRP434404\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"56\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"56\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"source_alias_confirmed","source_date":"2023-06-05","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP442922","agent_decision":"include_alias","extraction_status":"ok","title":"Vedolizumab efficacy is associated with decreased intracolonic dendritic cells, not memory T cells [P430]","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":96,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2023-08-27","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP443791","agent_decision":"include_alias","extraction_status":"ok","title":"Vedolizumab efficacy is associated with decreased intracolonic dendritic cells, not memory T cells [P444]","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":346,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2023-08-27","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP502014","agent_decision":"include_alias","extraction_status":"ok","title":"Ileal Enterocyte Brush Border Abnormalities Associate with Progressive Disease Course in Pediatric Crohn's Disease","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":152,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2025-12-18","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP534562","agent_decision":"include_alias","extraction_status":"ok","title":"Contribution of Stroma to Inflammatory Bowel Disease Progression Revealed in Patient-Derived Human Colon Chips","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":66,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2025-01-03","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP565898","agent_decision":"include_alias","extraction_status":"ok","title":"Single cell RNA sequencing of treatment naive Crohn's disease","summary":null,"study_type_class":"target_single_cell_rnaseq","technology_field":null,"target_sample_rows":95,"included_by_policy_rows":0,"raw_sample_rows":95,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2025-03-09","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP675345","agent_decision":"include_alias","extraction_status":"ok","title":"Multi-omic characterization of genetic variants in IBD risk loci","summary":null,"study_type_class":"target_rnaseq","technology_field":null,"target_sample_rows":189,"included_by_policy_rows":0,"raw_sample_rows":190,"default_region_counts_json":"[]","decision":"source_alias_confirmed","source_date":"2026-04-24","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP691165","agent_decision":"include_alias","extraction_status":"ok","title":"Improved Efficacy of Fecal Microbiota Transplantation for Ulcerative Colitis with Non-urbanized Donors","summary":null,"study_type_class":"targeted_amplicon","technology_field":null,"target_sample_rows":70,"included_by_policy_rows":0,"raw_sample_rows":593,"default_region_counts_json":"[{\"accession\": \"SRP691165\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"51\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"51\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"source_alias_confirmed","source_date":"2026-04-15","source_date_kind":"first_public_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-10832","agent_decision":"exclude","extraction_status":"ok","title":"RNA-seq of organoid derived monolayers (inflamed and non-inflamed) of UC patients and non-IBD controls, stimulated with microbiota of patients or a healthy donor","summary":"Dysbiosis is linked to the pathogenesis of inflammatory bowel disease. Although there is a lot of interest in restoring the balance, we do not understand the effects of dysbiosis, especially on epithelial cells. In addition, we know that epithelial cells from IBD patients maintain intrinsic defects. For that reason, we aimed to unravel if epithelial cells of UC patients are more sensitive towards microbiota stimulation, compared to non-IBD controls. In addition, we analyzed the effect of UC microbiota or microbiota of healthy donors towards epithelial cells. Confluent organoid derived monolayers of 8 UC patients and 8 non-IBD controls were co-cultured for 6 hours with microbiota (3.10^8 cells) , derived of a healthy donor (HD) or UC patients. If applicable, epithelial cells were first cultured for 24 hours with an inflammatory mix (100 ng/mL TNFα, 20 ng/mL IL1β, 1 µg/mL Flagellin). The inflammatory stimulation was continued in the 6 hours co-culture.Transcriptomic expression of epithelial cells was evaluated after 6 hours co-culture by Truseq for Illumina.","study_type_class":"target_rnaseq","technology_field":"BioStudies Source Characteristics","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":96,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2022-07-31","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-12841","agent_decision":"exclude","extraction_status":"ok","title":"Altered MHC class 1 DNA methylation of intestinal epithelial stem cells contributes to chronic inflammation in Crohn’s Disease","summary":"Altered function of the intestinal epithelium has been considered to play a key role in CD pathogenesis, however exact mechanisms that contribute towards lifelong relapsing mucosal inflammation remain ill defined. DNA methylation (DNAm) is a key epigenetic mechanism known to determine cellular identity by regulating gene transcription with alterations increasingly being implicated in IBD pathogenesis. We generated 312 intestinal epithelial organoids (IEOs) from mucosal stem cells obtained from 168 patients diagnosed with CD, non-IBD/healthy controls and Ulcerative colitis (UC). Genome wide epigenetic profiling of IEOs and primary purified epithelium revealed highly stable, CD associated loss of DNAm in MHC-I related genes which correlated with increased gene expression.  Related Single Cell Portal accession number: SCP1884 Related Gene Expression Omnibus accession numbers: GSE57945, GSE75214","study_type_class":"non_expression_dna_methylation","technology_field":"BioStudies Source Characteristics","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":312,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2024-03-31","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-5463","agent_decision":"exclude","extraction_status":"ok","title":"DNA methylation profiling of intestinal epithelial cells from paediatric biopsies including Inflammatory Bowel disease and healthy controls","summary":"We purified the intestinal epithelial cells from biopsies taken from the ileum and colon of a paediatric cohort of IBD patients and healthy controls","study_type_class":"non_expression_dna_methylation","technology_field":"BioStudies Source Characteristics","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":215,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2017-10-20","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-7860","agent_decision":"exclude","extraction_status":"ok","title":"RNA-seq of biopsies, crypts and organoids of inflamed and non-inflamed biopsies of ulcerative colitis patients","summary":"Patient-derived intestinal organoids provide an excellent tool to unravel mechanisms underlying ulcerative colitis (UC). Fresh biopsies, to isolate crypts and culture organoids, were obtained from both inflamed and non-inflamed regions from eight patients with active UC (Mayo endoscopic subscore ≥2), and from eight non-IBD controls.To address the inflammatory character of ex vivo organoids, we compared the transcriptome of biopsies, crypts and organoids derived from inflamed, and non-inflamed regions and aimed to (re-)induce inflammation ex vivo.","study_type_class":"target_rnaseq","technology_field":"BioStudies Source Characteristics","target_sample_rows":48,"included_by_policy_rows":0,"raw_sample_rows":144,"default_region_counts_json":"[{\"accession\": \"E-MTAB-7860\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"16\", \"other_uc\": \"32\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"16\", \"total_uc\": \"32\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2020-10-08","source_date_kind":"release_date"},{"source":"ARRAYEXPRESS","accession":"E-MTAB-8901","agent_decision":"exclude","extraction_status":"ok","title":"Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease","summary":"In this study, we performed single-cell transcriptional profiling of human embryonic and fetal gut samples obtained from 9 human embryos spanning ages 6-10 PCW and three regions (duo-jejunum, ileum and colon). Additionally, we profile mucosal biopsies from the terminal ileum of healthy children aged 4-12 years (n = 8) as well as a group of children newly diagnosed with Crohn’s disease (CD) (n = 7), a common form of IBD. Tissue samples were treated using an enzymatic dissociation protocol and single cell suspensions were then processed using the 3’v2 10x Genomics Chromium workflow. In a subset of samples, the intestinal epithelial cell fraction was enriched by performing magnetic bead sorting for EPCAM. In total, we generate single cell transcriptomes of ~90,000 primary human intestinal cells providing a rich resource and detailed roadmap. Using this data as well as scRNAseq profiles of human fetal gut derived organoids we describe embryonic and fetal epithelium composition, trace their differentiation dynamics and signaling partners, and provide links to regenerating Crohn’s disease epithelium.","study_type_class":"target_single_cell_rnaseq","technology_field":"BioStudies Source Characteristics","target_sample_rows":49,"included_by_policy_rows":26,"raw_sample_rows":55,"default_region_counts_json":"[{\"accession\": \"E-MTAB-8901\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"7\", \"ileum_control\": \"19\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"23\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"7\", \"total_control\": \"42\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2020-12-22","source_date_kind":"release_date"},{"source":"ENA","accession":"ERP186171","agent_decision":"exclude","extraction_status":"ok","title":"Valeric Acid in IBD","summary":"Illumina NovaSeq X sequencing","study_type_class":"target_rnaseq","technology_field":"ENA Portal read_run library_strategy/library_source","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":95,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2025-12-08","source_date_kind":"first_public_date"},{"source":"GEO","accession":"GSE114603","agent_decision":"exclude","extraction_status":"ok","title":"A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":38,"included_by_policy_rows":0,"raw_sample_rows":76,"default_region_counts_json":"[{\"accession\": \"GSE114603\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"6\", \"other_uc\": \"32\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"6\", \"total_uc\": \"32\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2018-11-06","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE125527","agent_decision":"exclude","extraction_status":"ok","title":"Single-Cell Analyses Elucidate the Cellular and Molecular Landscape of Ulcerative Colitis","summary":"Inflammatory bowel disease (IBD) encompasses a spectrum of complex intestinal disorders characterized by dysregulated host innate and adaptive immune responses to gut microbiota in genetically susceptible hosts. We generated an integrated single-cell (scRNA-seq, scTCR-seq, and scBCR-seq) resource dataset that revealed key cellular components and cell states of the gastrointestinal mucosal and peripheral immune systems in health and ulcerative colitis (UC).","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":41,"included_by_policy_rows":0,"raw_sample_rows":103,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2020-07-16","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE128449","agent_decision":"exclude","extraction_status":"ok","title":"Differences in expression profiling between tumoral colorectal carcinomas subsets and normal tissue and polyps","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":58,"included_by_policy_rows":0,"raw_sample_rows":84,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2019-03-19","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE135751","agent_decision":"exclude","extraction_status":"ok","title":"Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":59,"included_by_policy_rows":0,"raw_sample_rows":366,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2021-02-03","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE139680","agent_decision":"exclude","extraction_status":"ok","title":"Differences in microbiome populations following hematopoietic stem cell transplantation in Crohn?s disease patients","summary":"Treatment of severely refractory Crohn’s disease (CD) patients remains a clinical challenge. Recent studies show the efficacy of autologous hematopoietic stem cell transplant (HSCT) in these severely compromised patients. HSCT is thought to eliminate auto-reactive cells; however, no specific studies of immune reconstitution in CD patients are available. We studied a group of CD patients (n=18) receiving autologous HSCT. We studied changes in the microbiome induced by HSCT and some non-CD samples.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":158,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2020-10-22","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE14442","agent_decision":"exclude","extraction_status":"ok","title":"Gene expression analysis in gut biopsies of Crohn's Disease patients and patients with Spondylarthropathy","summary":"A focussed microarray chip was constructed specifically for studying basal colonic gene expression in patients with Spondyloarthropathy (SpA) and Crohn's disease (CD) (ref: PMID 16476712). These focus microarrays were used 1) to study common changes in gene expression between SpA and CD, providing early markers in the follow-up study of patients with SpA and particularly these patients that evolve into clinically overt CD; and 2) to identify new candidate genes for CD by integrating gene expression data with genetic information. Keywords: Crohn's Disease, Spondylarthropathy, biopsies","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":84,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2010-05-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE159010","agent_decision":"exclude","extraction_status":"ok","title":"Transcriptomic profiling of collagenous colitis identifies hallmarks of non-destructive inflammatory bowel disease","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":78,"included_by_policy_rows":0,"raw_sample_rows":78,"default_region_counts_json":"[{\"accession\": \"GSE159010\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"4\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"4\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2021-05-03","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE189185","agent_decision":"exclude","extraction_status":"ok","title":"Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis.","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_spatial_transcriptomics","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":82,"included_by_policy_rows":0,"raw_sample_rows":117,"default_region_counts_json":"[{\"accession\": \"GSE189185\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"29\", \"other_uc\": \"4\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"29\", \"total_uc\": \"4\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2024-04-12","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE215285","agent_decision":"exclude","extraction_status":"ok","title":"Regional transcriptomics and proteomics of DMPK genes in human intestine","summary":"The intestine is an organ responsible for absorption and metabolism of orally administered drugs. It is necessary to examine the human intestinal expression profiles of the genes related to drug absorption, distribution, metabolism, and excretion (ADME), for accurate prediction of pharmacokinetics in the intestine. However, previous studies had issues such as the evaluation limited to specific molecules and regions, and relatively small sample sizes. In this study, to obtain more accurate expression profiles of mRNA and protein in various regions of human intestine, biopsy samples were collected from 38 patients with various regions, duodenum, jejunum, ileum, colon and rectum, and RNA-seq analysis and quantitative proteomics analysis were performed. We performed the expression analysis of drug-metabolizing enzymes (cytochromes P450 (CYP ) and non–CYP enzymes), apical and basolateral drug transporters, and nuclear receptors. Overall, mRNA expression levels of these ADME-related molecules were highly correlated with the protein expression levels. The characteristics of the expression of ADME-related genes in human small and large intestines differed significantly, such as higher or lower expression levels of CYP enzymes in the small or large intestines, respectively. Most CYPs were expressed dominantly in the small intestine. Non-CYPs were expressed in the large intestine, but their expression levels were lower than those in the small intestine. The expression levels of ADME-related genes differed even between the proximal and distal small intestine. The expression of transporters showed their highest abundance in the ileum. The data in the present study contributes to an improved understanding of intestinal ADME of drug candidates, and would be useful for drug discovery research.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":61,"included_by_policy_rows":0,"raw_sample_rows":61,"default_region_counts_json":"[{\"accession\": \"GSE215285\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"12\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"12\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2023-05-08","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE246987","agent_decision":"exclude","extraction_status":"ok","title":"Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets","summary":"The pathophysiology of Crohn’s-like disease of the pouch (CDP) that develops after restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) is unknown. We examined mucosal cells from patients with and without CDP using single cell analyses.","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":22,"included_by_policy_rows":0,"raw_sample_rows":59,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2024-08-02","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE277964","agent_decision":"exclude","extraction_status":"ok","title":"Contribution of Stroma to Inflammatory Bowel Disease Progression Revealed in Patient-Derived Human Colon Chips","summary":"Inflammatory bowel disease (IBD) patients exhibit compromised intestinal barrier function, enhanced inflammation, and increased cancer risk, with symptoms sometimes being exacerbated in women during pregnancy. To investigate the IBD phenotype and disease progression in human intestine, we leveraged organ-on-a-chip (Organ Chip) technology to engineer human Colon Chips lined by homotypic or heterotypic recombinants of intestinal epithelium interfaced with stromal fibroblasts isolated from Healthy or IBD patient-derived colon resections. Chips created with both epithelial and stromal cells from the same ulcerative colitis or Crohn's disease patient showed increased IBD-associated gene pathway activation, elevated pro-inflammatory cytokines, reduced mucus layer thickness, increased intestinal barrier permeability, compared to homotypic Healthy Colon Chips. When heterotypic tissue recombinants were created, the IBD stromal fibroblasts induced the IBD phenotype in healthy epithelium, and healthy colonic fibroblasts partially reduced inflammation in the IBD epithelium. Using this system, we discovered that peristalsis-like mechanical deformations directly impact colon tissue physiology by increasing mucin gene expression, mucus thickness, and barrier permeability in both Healthy and IBD Chips, and that they only stimulate a fibrotic response in IBD Chips. We also found that both inflammation and fibrosis were accentuated in IBD Chips created with cells from a female patient that were exposed to pregnancy-associated hormones. Interestingly, exposure to a carcinogen (N-ethyl-N-nitrosourea) for 3 weeks in vitro induced histological changes and gene duplication in the IBD Chips, but not in the Healthy Chips. These data suggest that the stroma plays a key role in driving inflammation and disease progression in IBD patients and that human Organ Chip technology may represent a new preclinical tool to gain insight into these mechanisms as well as to identify novel diagnostic biomarkers and therapeutics.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":66,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2025-01-02","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE282444","agent_decision":"exclude","extraction_status":"ok","title":"Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [RNA-seq]","summary":"The pathogenesis of Inflammatory Bowel Disease (IBD) is a multifactorial process characterized by inflammation and damage to the intestinal barrier, which is made up of intestinal epithelial cells (IECs). Since IBD is a remitting and relapsing disease, we postulated that epigenetic memory exists in IECs following an inflammatory encounter. The objective of this study was to uncover the mechanisms of a retained altered IEC epigenetic landscape in the context of IBD. We have generated adult stem cell organoids (containing all epithelial cell lineages) from patients with Ulcerative Colitis (UC); two organoid lines per patient were propagated: 1) from a site of active inflammation and from the same patient, and 2) a never inflamed region. We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and bulk RNA-seq on each organoid line. Established bioinformatic pipelines were used to determine significantly different chromatin accessibility and differentially expressed genes. Functional significance of the open chromatin regions was assessed by pathway and motif analysis. Treatment with TNF-alpha (10 and 100ng/ml) for 24 hours on the organoids was performed to determine re-activation of pro-inflammatory genes. This study shows for the first time that epithelial cells derived from organoids of IBD patients retain an epigenetic memory of the prior inflammatory state.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":56,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2026-02-28","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE288179","agent_decision":"exclude","extraction_status":"ok","title":"Differential response of patient-derived intestinal organoids to site-specific mucosal bacteria in pediatric inflammatory bowel disease","summary":"Objective: Inflammatory bowel disease (IBD) is secondary to an abnormal immune response to the microbiota. There is evidence of impaired stem cell signatures in IBD contributing to impaired epithelial repair. We therefore aimed to study the role of the microbiome in the intestinal stem cell population in paediatric IBD cases, a group without confounding treatments or comorbidities, by directly studying the interaction between patient-isolated bacteria and the epithelium. Design: We established a unique biobank with matched intestinal organoids and cultured mucosally adherent bacteria from 36 paediatric patients. To determine the bacterial effect on host epithelial cells, closely related bacterial isolates from control and IBD patients were selected for microinjection into their corresponding organoid line. Results: Whilst no differences were observed between control and IBD-derived organoids following injury, transcriptional profiling revealed differential gene expression between uninjured control and IBD- derived organoids. Furthermore, following microinjection of an isolate originating from a control patient, there was upregulation of inflammatory signalling pathways, whereas this was not observed with a closely related isolate originating from an IBD patient. Conclusion: This demonstrates the feasibility of isolating bacteria and generating organoids from the same biopsy tissue, to explore personalised host-microbe interactions. The microinjections show the individual nature of responses, with closely related bacteria inducing very different epithelial responses, with downstream implications for immune response. This highlights the importance of understanding host-microbe interactions in a strain and site-specific manner, and developing techniques for personalised microbiome-based therapeutics.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":105,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2025-10-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE29703","agent_decision":"exclude","extraction_status":"ok","title":"Association of microRNAs with CD68 and NOS2 in IBD tissues.","summary":"We analyzed the association of CD68 and NOS2 mRNA expression with microRNAs in IBD tissues. For this analysis, data was LOESS normalized in R. Data was then imported into Partek Genomics Suite and Batch effects caused by day to day variability (Dategroup of array charateristic) were corrected. We did not have mRNA expression data for CD68 and NOS2 for all of the samples, therefore those samples were not used for analysis. We identified several microRNAs associated with CD68 and NOS2 expression.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":114,"included_by_policy_rows":0,"raw_sample_rows":114,"default_region_counts_json":"[{\"accession\": \"GSE29703\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"52\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"52\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2012-08-01","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE305528","agent_decision":"exclude","extraction_status":"ok","title":"An epigenetic basis for sustained inflammatory epithelial progenitor cell states in Crohn’s disease","summary":"Defining consequential differences in intestinal epithelial stem cells in healthy humans versus those with inflammatory bowel disease (Crohn’s disease (CD) and ulcerative colitis) is essential for the development of therapies to restore the epithelial barrier and maintain its fidelity post-injury. Our study objective was to define transcriptomic, epigenomic, and functional divergence between healthy and CD epithelium.","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":0,"included_by_policy_rows":0,"raw_sample_rows":69,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2025-12-31","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE312415","agent_decision":"exclude","extraction_status":"ok","title":"Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [CosMx]","summary":"Spatial transcriptomics is a rapidly growing field with the potential to enhance our ability to uncover novel biology, support drug development, and guide biomarker discovery. However, a biologically validated comparison of leading single-cell-level spatial transcriptomics platforms to guide scientists is lacking in the field. Using intestinal biopsies (n = 40) from patients with inflammatory bowel disease (IBD) of varying disease states and disease locations and non-diseased controls, we systematically compared two imaging based spatial transcriptomics platforms (CosMx and Xenium) to guide translational work for two NIDDK supported IBD consortiums and the Crohn’s and Colitis Foundation Plexus Biorepository. In vitro experiments were conducted to validate key biologic findings. We present a comprehensive data resource of over 1.5 million spatially profiled intestinal cells from healthy and IBD samples. We observed CosMx to have overall better data quality than Xenium in both ulcerative colitis and Crohn’s disease across the full spectrum of commercially available panels. The performance of Xenium, but not CosMx, was significantly influenced by block quality and panel size, with a decline in data quality as the panel size increased. We demonstrate operational feasibility for CosMx in multi-center studies, and CosMx uniquely identified Treg-associated biology in both ulcerative colitis and Crohn’s disease which was validated by in vitro experiments. This study highlights the performance differences between CosMx and Xenium, demonstrating the strengths of CosMx for biology discovery in IBD research. Further studies are needed to explore the broader applicability of CosMx in other gastrointestinal conditions.","study_type_class":"target_single_cell_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":60,"included_by_policy_rows":2,"raw_sample_rows":60,"default_region_counts_json":"[{\"accession\": \"GSE312415\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"2\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"2\", \"other_control\": \"0\", \"other_uc\": \"6\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"4\", \"total_control\": \"0\", \"total_uc\": \"6\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2026-03-13","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE66209","agent_decision":"exclude","extraction_status":"ok","title":"mRNA and small RNA associated with Crohn's disease behavior","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":33,"included_by_policy_rows":0,"raw_sample_rows":74,"default_region_counts_json":"[{\"accession\": \"GSE66209\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"13\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"13\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2015-07-15","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE85499","agent_decision":"exclude","extraction_status":"ok","title":"Molecular classification of Crohn’s disease reveals two clinically relevant subtypes","summary":"Objective: The clinical presentation and course of Crohn’s disease (CD) is highly variable. We sought to better understand the cellular and molecular mechanisms that guide this heterogeneity, and characterize the cellular processes associated with disease phenotypes. Design: We examined both gene expression and gene regulation (chromatin accessibility) in non-inflamed colon tissue from a cohort of adult CD and control patients. To support the generality of our findings, we analyzed previously published expression data from a large cohort of treatment-naïve pediatric CD and control ileum. Results: We found that adult CD patients clearly segregated into two classes based on colon tissue gene expression—one that largely resembled the normal colon and one where certain genes showed expression patterns normally specific to the ileum. These classes were supported by changes in gene regulatory profiles observed at the level of chromatin accessibility, reflective of a fundamental shift in underlying molecular phenotypes. Further, gene expression from the ilea of the treatment-naïve pediatric CD patient cohort could be similarly subdivided into colon- and ileum-like classes. Finally, expression patterns within these CD subclasses highlight large-scale differences in the immune response and aspects of cellular metabolism, and were associated with multiple clinical phenotypes describing disease behavior, including rectal and perianal disease and need for colectomy. Conclusion: Our results strongly suggest that these molecular signatures define two clinically relevant forms of CD irrespective of tissue sampling location, patient age or treatment status.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":32,"included_by_policy_rows":0,"raw_sample_rows":53,"default_region_counts_json":"[{\"accession\": \"GSE85499\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"21\", \"other_control\": \"11\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"21\", \"total_control\": \"11\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2016-12-11","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE95459","agent_decision":"exclude","extraction_status":"ok","title":"Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease","summary":"This SuperSeries is composed of the SubSeries listed below.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":480,"included_by_policy_rows":0,"raw_sample_rows":480,"default_region_counts_json":"[{\"accession\": \"GSE95459\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"288\", \"other_uc\": \"64\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"288\", \"total_uc\": \"64\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2018-09-26","source_date_kind":"release_date"},{"source":"HCA","accession":"23509202-1E3C-4959-8A45-9C5B642A1066","agent_decision":"exclude","extraction_status":"ok","title":"Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses","summary":"Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal mucosal immune systems in health and ulcerative colitis (UC). UC was associated with an increase in IgG1+ plasma cells in colonic tissue, increased colonic regulatory T cells characterized by elevated expression of the transcription factor ZEB2, and an enrichment of a γδ T cell subset in the peripheral blood. Moreover, we observed heterogeneity in CD8+ tissue-resident memory T (TRM) cells in colonic tissue, with four transcriptionally distinct states of differentiation observed across health and disease. In the setting of UC, there was a marked shift of clonally related CD8+ TRM cells toward an inflammatory state, mediated, in part, by increased expression of the T-box transcription factor Eomesodermin. Together, these results provide a detailed atlas of transcriptional changes occurring in adaptive immune cells in the context of UC and suggest a role for CD8+ TRM cells in IBD.","study_type_class":"target_single_cell_rnaseq","technology_field":"HCA Azul sample index metadata","target_sample_rows":60,"included_by_policy_rows":16,"raw_sample_rows":103,"default_region_counts_json":"[{\"accession\": \"23509202-1E3C-4959-8A45-9C5B642A1066\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"16\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"24\", \"other_uc\": \"0\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"40\", \"total_uc\": \"0\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2021-06-11","source_date_kind":"submission_date"},{"source":"SRA","accession":"PRJNA1450848","agent_decision":"exclude","extraction_status":"ok","title":"Improved Efficacy of Fecal Microbiota Transplantation for Ulcerative Colitis with Non-urbanized Donors","summary":"Illumina NovaSeq 6000 sequencing: human intestinal mucosa 16S","study_type_class":"targeted_amplicon","technology_field":"ENA Portal read_run library_strategy/library_source","target_sample_rows":70,"included_by_policy_rows":0,"raw_sample_rows":593,"default_region_counts_json":"[{\"accession\": \"PRJNA1450848\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"51\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"51\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"reject_confirmed","source_date":"2026-04-15","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP362044","agent_decision":"exclude","extraction_status":"ok","title":"Transcriptional and functional characterization of human intestinal organoid and monolayer models for IBD-therapeutic development","summary":"Illumina NovaSeq 6000 sequencing: GSM5928408: HFO_FP_b001_9_cbc Homo sapiens RNA-Seq","study_type_class":"target_rnaseq","technology_field":"ENA Portal read_run library_strategy/library_source","target_sample_rows":211,"included_by_policy_rows":0,"raw_sample_rows":211,"default_region_counts_json":"[]","decision":"reject_confirmed","source_date":"2023-02-09","source_date_kind":"first_public_date"},{"source":"GEO","accession":"GSE118754","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"Transcriptome Expression Data from Resected Operative Ileal Mucosa Specimens in a cohort of patients with Crohns Disease","summary":"Affymetrix human whole transcriptome array (HTA 2.0) completed on patients with Crohn's disease undergoing their first ileocolic resection","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":65,"included_by_policy_rows":0,"raw_sample_rows":65,"default_region_counts_json":"[]","decision":"metadata_unavailable","source_date":"2018-08-21","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE282580","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"Colon tissue gene expression associated with vedolizumab treatment effectiveness in ulcerative colitis.","summary":"Transcriptional profiling was performed on colorectal tissues, both inflammatory and non-inflammatory, collected from patients with ulcerative colitis.","study_type_class":"target_rnaseq","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":120,"included_by_policy_rows":0,"raw_sample_rows":120,"default_region_counts_json":"[{\"accession\": \"GSE282580\", \"ascending_cd\": \"0\", \"ascending_control\": \"0\", \"ascending_uc\": \"0\", \"descending_cd\": \"0\", \"descending_control\": \"0\", \"descending_uc\": \"0\", \"ileum_cd\": \"0\", \"ileum_control\": \"0\", \"ileum_uc\": \"0\", \"other_cd\": \"0\", \"other_control\": \"0\", \"other_uc\": \"60\", \"sigmoid_cd\": \"0\", \"sigmoid_control\": \"0\", \"sigmoid_uc\": \"0\", \"total_cd\": \"0\", \"total_control\": \"0\", \"total_uc\": \"60\", \"transverse_cd\": \"0\", \"transverse_control\": \"0\", \"transverse_uc\": \"0\"}]","decision":"metadata_unavailable","source_date":"2025-08-25","source_date_kind":"release_date"},{"source":"GEO","accession":"GSE65270","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.","summary":"Pouchitis is a common complication for ulcerative colitis (UC) patients with ileal pouch-anal anastomosis (IPAA) surgery. Similarly to IBD, both innate host factors such as genetics, and environmental stimuli including the tissue-associated microbiome have been implicated in the pathogenesis. In this study, we make use of the IPAA model of inflammatory bowel disease (IBD) to carry out a study associating mucosal host gene expression with the microbiome and corresponding clinical outcomes.","study_type_class":"target_expression_array","technology_field":"GEO DataSet Type / Platform Technology Type","target_sample_rows":273,"included_by_policy_rows":0,"raw_sample_rows":273,"default_region_counts_json":"[]","decision":"metadata_unavailable","source_date":"2015-01-27","source_date_kind":"release_date"},{"source":"SRA","accession":"PRJNA1206238","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"Multi-omic characterization of genetic variants in IBD risk loci","summary":"Illumina NovaSeq X sequencing: RNA-seq on inflammatory bowel disease colon tissue","study_type_class":"target_rnaseq","technology_field":"ENA Portal read_run library_strategy/library_source","target_sample_rows":189,"included_by_policy_rows":0,"raw_sample_rows":190,"default_region_counts_json":"[]","decision":"metadata_unavailable","source_date":"2026-04-24","source_date_kind":"first_public_date"},{"source":"SRA","accession":"PRJNA1227436","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"Single cell RNA sequencing of treatment naive Crohn's disease","summary":"Illumina NovaSeq 6000 sequencing: single cell RNA seq of Homo sapiens: pediatric ileum","study_type_class":"target_single_cell_rnaseq","technology_field":"ENA Portal read_run library_strategy/library_source","target_sample_rows":95,"included_by_policy_rows":0,"raw_sample_rows":95,"default_region_counts_json":"[]","decision":"metadata_unavailable","source_date":"2025-03-09","source_date_kind":"first_public_date"},{"source":"SRA","accession":"PRJNA774132","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"RNA-seq of Korean Inflammatory Bowel Disease tissues","summary":"Illumina NovaSeq 6000 sequencing: RNA-seq of human IBD patients: colon","study_type_class":"target_rnaseq","technology_field":"ENA Portal read_run library_strategy/library_source","target_sample_rows":127,"included_by_policy_rows":0,"raw_sample_rows":127,"default_region_counts_json":"[]","decision":"metadata_unavailable","source_date":"2021-12-14","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP173349","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"Characterising the Gut Microbial Ecosystem for Diagnosis and Therapy in IBD","summary":"Illumina HiSeq 2000 sequencing: Reduced Representation Bisulfite Sequencing (RRBS) libraries: Ileum biopsy: Sample M2026CSC3_RRBS","study_type_class":"non_expression_dna_methylation","technology_field":"ENA Portal read_run library_strategy/library_source","target_sample_rows":251,"included_by_policy_rows":0,"raw_sample_rows":793,"default_region_counts_json":"[]","decision":"metadata_unavailable","source_date":"2020-04-22","source_date_kind":"first_public_date"},{"source":"SRA","accession":"SRP572305","agent_decision":"metadata_unavailable","extraction_status":"metadata_unavailable","title":"Single cell and spatial transcriptomics studies of Fibrosis in Prospective Registry in IBD Study at MGH and GI Disease and Endoscopy Registry","summary":"Illumina HiSeq X sequencing: Intestinal tissue sample was processed within 3 hours of collection with epithelial stripping followed by collagenase digestion to generate a single cell suspension 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