|
Status |
Public on Sep 26, 2018 |
Title |
20141211_C10 |
Sample type |
SRA |
|
|
Source name |
colonic mucosa
|
Organism |
Homo sapiens |
Characteristics |
disease: healthy sample_type: single cell donor_id: p6
|
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_711507
|
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 |
SRX2596054 |
BioSample |
SAMN06472091 |