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Sample GSM3214204 Query DataSets for GSM3214204
Status Public on Feb 27, 2019
Title B3_inflamed
Sample type SRA
Source name UC_inflamed
Organism Homo sapiens
Characteristics subject status: Ulcerative colitis
tissue: inflamed area of colon
cell type: epithelial cells
Treatment protocol n/a
Growth protocol n/a - no samples were cultured
Extracted molecule total RNA
Extraction 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. 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description B3_inflamed
Data processing Basecalling was performed using Illumina Casava software
Samples were demultiplexed using Illumina bcl2fasq software
Sequenced reads were processed, aligned and counts summarised using Cellranger 2.1 pipeline
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited UMI counts per  10,000 unique molecules detected
Submission date Jun 25, 2018
Last update date Feb 27, 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
Platform ID GPL24676
Series (1)
GSE116222 Colonic single epithelial cell census reveals goblet cell drivers of barrier breakdown in inflammatory bowel disease
BioSample SAMN09479598
SRA SRX4291261

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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