|
| Status |
Public on Sep 26, 2018 |
| Title |
20160513_C68 |
| Sample type |
SRA |
| |
|
| Source name |
colonic mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
disease: ulcerative colitis
sample_type: single cell
donor_id: p13
endoscopic_appearance: Inflamed
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_203207
|
| 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 |
SRX2597798 |
| BioSample |
SAMN06467375 |
