|
| Status |
Public on May 05, 2024 |
| Title |
ATAC-Seq EpCam_High_CK19_02 |
| Sample type |
SRA |
| |
|
| Source name |
primary liver cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: liver
|
| Treatment protocol |
none
|
| Growth protocol |
primary liver cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cell suspension are obtained by enzymatic digestion of liver or macroscopic lesions. YFP+ cells (indicative of efficient Cre-mediated recombination of floxed alleles) are isolated by Flow cytometry for further processing.
standard protocol for bulk ATAC-Seq preparation were used for library construction and sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
EpCam_High_CK19_02
|
| Data processing |
after trimming the adapters with attack (version 0.1.5 – https://atactk.readthedocs.io/en/latest/index.html), the raw reads were aligned to the mm10 genome using bowtie-1.1.2 (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25) with the following flags: --chunkmbs 2000 --sam --best --strata --ml -X2000. We used MACS2 for peak calling with a q cutoff of 0.05. Downstream analysis and visualization was performed using HOMER and deepTools.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files denoting significant regions of open chromatin (obtained with macs2)
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
May 05, 2024 |
| Contact name |
Patrick Viatour |
| E-mail(s) |
viatourp@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Street address |
3501 Civic Center Blvd
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE173948 |
Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (ATAC-Seq) |
| GSE173952 |
Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model |
|
| Relations |
| BioSample |
SAMN19025549 |
| SRA |
SRX10786619 |
