|
| Status |
Public on Aug 20, 2020 |
| Title |
BA_P7_HSC_U6 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
age: P7
genotype: Wildtype
cell type: Hematopoietic stem cell
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
U6
Processed data file: BA_P7_HSC.fc.signal.bigwig
Processed data file: BA_P7_HSC.optimal_peak.narrowPeak.gz
|
| Data processing |
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by bowtie2 (versoin 2.2.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab ATAC-seq and DNase-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines, version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak
|
| |
|
| Submission date |
Oct 04, 2019 |
| Last update date |
Aug 20, 2020 |
| Contact name |
Jeffery Magee |
| E-mail(s) |
magee_j@kids.wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Internal Medicine - Cardiovascular Division
|
| Street address |
660 S Euclid Ave.
|
| City |
St Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE128758 |
Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution (ATAC-seq) |
| GSE128762 |
Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution |
|
| Relations |
| BioSample |
SAMN12912800 |
