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Series GSE116222 Query DataSets for GSE116222
Status Public on Feb 27, 2019
Title Colonic single epithelial cell census reveals goblet cell drivers of barrier breakdown in inflammatory bowel disease
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We report the results of 3 single cell RNA-sequencing (10x, chromium) experiments looking to characterise the composition of the intestinal epithelial cells in health and Ulcerative Colitis in order to identify drivers of intestinal inflammation at the molecular level. The data in this submission comprises of 3 repeat experiments (A, B, C) with biopsy samples taken from colonic biopsies collected from healthy patients (Healthy) and those with UC inflammation from an inflamed area of colon and adjacent non-inflamed area. All biopsies underwent and epithelial cell isolation protocol by digestion and then were loaded onto the 10x single cell RNA sequencing platform with subsequent GEM generation, cDNA isolation, amplification and library construction into one library using illumina barcodes. A single library was then sequenced on a NovaSeq 6000
Overall design single cell RNA-sequencing on intestinal epitehlial cells from healthy controls and Ulcerative colitis
Contributor(s) Parikh K, Antanaviciute A, Fawkner-Corbett D, Jagielowicz M, Kinchen J, Aulicino A, Ashley N, Johnson E, Hublitz P, Bao L, Andev RS, Bjorkland E, Koohy H, Simmons A
Citation(s) 30814735
Submission date Jun 25, 2018
Last update date Mar 04, 2019
Contact name Alison Simmons
Organization name University of Oxford
Department The MRC Weatherall Institute of Molecular Medicine
Street address John Radcliffe Hospital/Headley Way
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (9)
GSM3214201 A3_inflamed
GSM3214202 A2_non_inflamed
GSM3214203 A1_healthy
BioProject PRJNA477814
SRA SRP151260

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE116222_Expression_matrix.txt.gz 176.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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