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SRX4291260: GSM3214203: A1_healthy; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 186.8M spots, 28G bases, 5.8Gb downloads

Submitted by: NCBI (GEO)
Study: Colonic single epithelial cell census reveals goblet cell drivers of barrier breakdown in inflammatory bowel disease
show Abstracthide Abstract
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
Sample: A1_healthy
SAMN09479599 • SRS3454422 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: After study ethical approval fresh intestinal biopsies were collected during colonoscopy in those undergoing routine / screening colonoscopy (Healthy) of in those with known ulcerative colitis (UC). Samples were transported on ice and epithelial crypts isolated using a chelation medium (HPGA with 1mM EDTA) and then isolated crypts digested to a single cell solution (TryPLE Express with DNAse) before being processed in 10X chromium as per manufacturers protocol. Library construction by 3' prime V2 chemistry Chromium single cell gene expression kit. 
Experiment attributes:
GEO Accession: GSM3214203
Links:
Runs: 1 run, 186.8M spots, 28G bases, 5.8Gb
Run# of Spots# of BasesSizePublished
SRR7420402186,790,24028G5.8Gb2019-02-27

ID:
5778645

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