|
Status |
Public on Feb 27, 2019 |
Title |
C1_healthy |
Sample type |
SRA |
|
|
Source name |
healthy_colon
|
Organism |
Homo sapiens |
Characteristics |
subject status: healthy control tissue: colonic biopsy 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 |
C1_healthy
|
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 |
E-mail(s) |
alison.simmons@ndm.ox.ac.uk
|
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 |
|
Relations |
BioSample |
SAMN09479593 |
SRA |
SRX4291266 |