|
| Status |
Public on Nov 19, 2024 |
| Title |
CID003382-1-reup |
| Sample type |
SRA |
| |
|
| Source name |
gut
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: gut
librarytype: 3 prime V3
cellsloaded: 10000
disease: CD
disease duration: 228
patient: CD2
site: Terminal_Ileum
inflammation: Inflamed
treatment: Post
age: 37
Sex: M
ethnicity: Caucasian
match: Yes
batch: Batch_1
inflammation score: 5.5899704
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gut and synovial tissue samples and PBMCs were thawed into warm IMDM media with 10% FBS and washed. Gut samples were EDTA-treated pre-digestion with rotation for 15 min to remove dead/damaged epithelial cells, and then dissociated enzymatically with Liberase TM and DNase into a single-cell suspension with rotation. Thawed synovial samples were digested in Liberase TL and DNase in warm media for 30 min, with agitation. All cell samples were strained and washed twice with PBS with 0.4% bovine serum albumin (BSA). Live cells were counted using acridine orange/propidium iodide and ≤ 10,000 cells were loaded per 10X Chromium channel.
The GEX 3’ V3 protocol was followed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Cell Ranger v3.1.0 was used to align reads to reference (GRCh38-3.0.0) and generate feature- barcode matrices from the Chromium single-cell RNA-seq output.
Assembly: GRCh38-3.0.0
Supplementary files format and content: We have provided filtered matrices containing the outputs of the Cell Ranger pipeline in .h5 format for each sample as outlined above.
|
| |
|
| Submission date |
Nov 17, 2024 |
| Last update date |
Nov 19, 2024 |
| Contact name |
Tom Thomas |
| Organization name |
University of Oxford
|
| Street address |
Old Road Campus, Roosevelt Dr, Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7FY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE282122 |
A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease |
|
| Relations |
| BioSample |
SAMN44491583 |
| SRA |
SRX26530539 |
