|
| Status |
Public on Sep 17, 2021 |
| Title |
scRNA.CTRL |
| Sample type |
SRA |
| |
|
| Source name |
Ex vivo samples from pancreas
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary pancreatic epithelial cells
growth protocol: Ex vivo samples, no need to grow
treatment: Untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreata were harvested from C57BL/6J wild-type mice at different time points before and after acute inflammation and digested to obtain single cell suspension. After depletion of CD45-positive cells, primary cells derived from 3 pancreata were mixed for each time point, and 10,000 cells were captured followed by library preparation using 10X Chromium single cell 3’ V3 chemistry according to manufacturer’s protocol. Libraries were then multiplexed and sequenced on a single lane of NovaSeq6000 S2‐100 flow cell (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw sequencing data were pre- processed (demultiplexed cellular barcodes, read alignment, and generation of gene count matrix) using Cell Ranger Single Cell Software Suite provided by 10x Genomics. Detailed QC metrics were generated and evaluated. Genes detected in <0.1% of total sequenced cells and cells where < 200 genes had nonzero counts were filtered out and not included in the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: matrix counts
|
| |
|
| Submission date |
Aug 01, 2021 |
| Last update date |
Sep 17, 2021 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
|
| Organization name |
IRCCS San Raffaele Scientific Institute
|
| Department |
Center for Omics Sciences
|
| Street address |
Via Olgettina 58
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE180212 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis |
| GSE181276 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis [scRNA-Seq] |
|
| Relations |
| BioSample |
SAMN20516125 |
| SRA |
SRX11623884 |
