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Series GSE95450 Query DataSets for GSE95450
Status Public on Sep 26, 2018
Title Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [3]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Intestinal health is sustained by cooperation between diverse cell types, including epithelial cells, immune cells and stromal cells. Colonic stromal cells provide critical structural support but also regulate mucosal immunity, tolerance and inflammatory responses. Although mucosal stromal cells display substantial variability and plasticity, a paucity of unique genetic markers has precluded the identification of distinct stromal populations and functions. We used single-cell RNA-sequencing to uncover heterogeneity and subtype-specific markers of individual colonic stromal cells in health and ulcerative colitis (UC). Marker-free transcriptional clustering revealed four distinct stromal populations in healthy colon, corresponding to myofibroblasts and three previously unknown distinct subsets of fibroblasts. These fibroblast subsets were substantially remodeled in UC compared to healthy colon: inflamed UC colon was depleted for a healthy fibroblast subpopulation associated with epithelial cell homeostasis, and enriched for a novel disease-associated subtype expressing pro-inflammatory genes. Thus, we have discovered new, molecularly distinct colonic stromal cell subtypes that are altered in human disease.
 
Overall design Ulcerative colitis colonic lamina propria mesenchymal cells from 3 donors. 178 single cell libraries, 7 bulk controls, 7 empty well controls. Individual donors processed as separate batches on Fluidigm C1 IFCs and pooled for sequencing (1 x Illumina HiSeq 4000 lane).
 
Contributor(s) Kinchen J, Simmons A
Citation(s) 30270042
Submission date Feb 27, 2017
Last update date May 15, 2019
Contact name James Kinchen
E-mail(s) james.kinchen@stx.ox.ac.uk
Organization name University of Oxford
Department Nuffield Department of Medicine
Lab Alison Simmons
Street address Weatherall Institute of Molecular Medicine, John Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (192)
GSM2514289 20151130_C02
GSM2514290 20151130_C27
GSM2514291 20151130_C64
This SubSeries is part of SuperSeries:
GSE95459 Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Relations
BioProject PRJNA377153
SRA SRP100795

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE95450_P160099_full_gene_count_table.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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