|
Status |
Public on Mar 06, 2024 |
Title |
Healthy mouse liver CV-2 |
Sample type |
SRA |
|
|
Source name |
Liver
|
Organism |
Mus musculus |
Characteristics |
tissue: Liver tissue zone: CV 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 |
SAMN30809758 |
SRA |
SRX17535536 |