|
Status |
Public on Sep 26, 2018 |
Title |
20151130_C16 |
Sample type |
SRA |
|
|
Source name |
colonic mucosa
|
Organism |
Homo sapiens |
Characteristics |
disease: ulcerative colitis sample_type: single cell donor_id: p12 endoscopic_appearance: Uninflamed rna_fixative_used: none
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Endoscopic forceps biopsies were dissociated using a combined enzymatic and mechanical approach. Depletion of non-stromal cell types was achieved by MACS separation. CD326 (EpCAM), CD45 and CD235a conjugated micro-beads were added to the cell suspension, Cells were incubated with microbeads, washed and loaded onto an LD column via a 35 µm pre-separation filter. The flow-through fraction was collected, and single cells pelleted by centrifugation at 500 G for 8 minutes. Biopsies from inflamed and non-inflamed bowel regions were collected separately from the same donor, and single cell isolation was performed for both sets of biopsies in parallel. The resulting single cell suspensions were counter-stained and mixed 1:1 immediately prior to loading onto the C1 IFC. Nextera XT library prep kit (Illumina)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
processed data file header: WTCHG_288196_226201
|
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 |
GPL20301 |
Series (2) |
GSE95450 |
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [3] |
GSE95459 |
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease |
|
Relations |
SRA |
SRX2597777 |
BioSample |
SAMN06467426 |