|
| 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 |
| E-mail(s) |
[email protected]
|
| 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 |
SAMN09479598 |
| SRA |
SRX4291261 |
