|
| Status |
Public on Mar 10, 2021 |
| Title |
intestinal stromal cells pre-capture [WTCHG_288196_249227] |
| Sample type |
SRA |
| |
|
| Source name |
colonic mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
library: pre-capture
cell type: intestinal stromal cells
donor_id: p14
endoscopic_appearance: Inflamed
|
| Treatment protocol |
non
|
| Growth protocol |
cell isolation protocol is described in Kinchen et.al., Cell, 2018; PMID: 30270042
|
| Extracted molecule |
total RNA |
| Extraction protocol |
protocol is described in Kinchen et.al., Cell, 2018; PMID: 30270042
Pre-capture libraries were prepared following the 10x droplet-based protocol as described in Kinchen et.al., Cell, 2018; PMID: 30270042. Post-capture libraries were sequenced on 1 lane of a HiSeq 4000 at 75 bp paired end
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
counts_genes_symbols_PREcapture_GI.csv
|
| Data processing |
RNA-seq data were mapped to the hg38 assembly via STAR version 2.4.2
ribosomal rRNA was removed with the SortMeRNA version 2.1
read quality check with FastQC Version 0.10.1
read alignment quatification into gene counts with featureCount of Subread version 1.4.0
We excluded libraries with less than 2000 expressed genes; low complexity, where the % of 200 most expressed features represented more than 50% of total number of counts
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary files of raw counts are tab-delimited text files
|
| |
|
| Submission date |
Mar 10, 2021 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Alexandra Pokhilko |
| Organization name |
University of Oxford
|
| Department |
Nuffield Department of Clinical Neurosciences
|
| Street address |
John Radcliffe Hospital, Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE168626 |
Targeted single cell RNA-sequencing of transcription factors facilitates biological insights from human cell experimental models [intestinal stromal cells pre-capture] |
| GSE168634 |
Targeted single-cell RNA sequencing of transcription factors facilitates biological insights from human cell experimental models |
|
| Relations |
| BioSample |
SAMN18241621 |
| SRA |
SRX10304263 |
