|
| Status |
Public on Mar 06, 2024 |
| Title |
Healthy mouse liver PV-2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
tissue zone: PV
cell type: CD45+ cells
genotype: PA-GFP C57BL/6
treatment: Photoactivation
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
Single-cell RNA library construction was processed through the 10x Genomics Chromium Controller following the protocol outlined in the Chromium Next GEM Single Cell 3สน Reagent Kits v3.1 User Guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger count pipeline (cellranger-4.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: mm10
Supplementary files format and content: comma-delimited text files include raw counts for all cells detected
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Daisuke Motooka |
| E-mail(s) |
dry_team@ngs.gen-info.osaka-u.ac.jp
|
| Organization name |
NGS core facility, Research Institute for Microbial Diseases, Osaka University
|
| Street address |
3-1, Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE213165 |
Periportal macrophages protect against commensal-driven liver inflammation |
|
| Relations |
| BioSample |
SAMN30809759 |
| SRA |
SRX17535535 |
