|
| Status |
Public on Oct 02, 2020 |
| Title |
PHx, 72hr_scATAC |
| Sample type |
SRA |
| |
|
| Source name |
liver hepatocytes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
age: 10-12 weeks old
time point: 72h
protocol: PHx surgery
|
| Treatment protocol |
10-12 weeks old mice underwent partial hepatectomy surgery
|
| Growth protocol |
Mice were fed with normal diet
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hepatocytes were isolated using two-step collagenase perfusion method
scATAC-seq libraries were prepared for sequencing according to the Chromium Single Cell ATAC Reagent Kits User Guide v1 Chemistry
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
72h post-PHx surgery
|
| Data processing |
The Cell Ranger ATAC Software Suite was used for demultiplexing sequencing information
Nuclei were filtered with unique fragments greater than 1000 and TSS enrichment greater than 4
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files contain the peak calling results for pre- and post-PHx samples, respectively.
|
| |
|
| Submission date |
Oct 01, 2020 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Anna Mae Diehl |
| Organization name |
Duke University
|
| Street address |
Research Drive
|
| City |
Durham |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE158873 |
Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [scATAC-Seq] |
| GSE158874 |
Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration |
|
| Relations |
| BioSample |
SAMN16327842 |
| SRA |
SRX9228267 |
