|
| Status |
Public on Sep 26, 2018 |
| Title |
20141208_C16 |
| Sample type |
SRA |
| |
|
| Source name |
colonic mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
disease: healthy
sample_type: single cell
donor_id: p5
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Endoscopic forceps biopsies were incubated with 1mM EDTA with vigorous shaking to detach intact crypt units. Intact crypts separated from single cells and debris by centrifugation of the supernatant (150 G for 4 minutes). The crypt pellet was re-suspended in TrypLE Express (Thermo Fisher) supplemented with 50 ug/ml DNAse and incubated at 37C for 60 minutes, vortexing every 15 minutes. A pellet of dissociated single cells was obtained by passing the resultant suspension through a 35 um cell strainer and centrifugation of the filtrate at 500 G for 5 minutes.
Nextera XT library prep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file column header: WTCHG_168020_706505
|
| Data processing |
Trimming of adaptor sequences (IlluminaP7, Nextera, SMARTer) - skewer (https://github.com/relipmoc/skewer)
Alignment to human genome (Ensembl GRCh38) - HISAT (v2.0.3b)
Gene count table assembly (Ensembl Release 84, March 2016 transcriptome annotation) - featureCounts (v1.5.0)
Genome_build: Ensembl GRCh38
|
| |
|
| Submission date |
Feb 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
James Kinchen |
| E-mail(s) |
james.kinchen@stx.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Nuffield Department of Medicine
|
| Lab |
Alison Simmons
|
| Street address |
Weatherall Institute of Molecular Medicine, John Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE95435 |
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [1] |
| GSE95459 |
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease |
|
| Relations |
| SRA |
SRX2596012 |
| BioSample |
SAMN06472184 |
