|
| Status |
Public on Aug 20, 2020 |
| Title |
P14_HSC-1 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Hematopoietic stem cell
age: P14
|
| 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 |
P14_HSC1
processed data in series file adult_HSC.pooled.fc.signal.bigwig
processed data in series file adult_HSC.filt.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 |
Mar 24, 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 |
SAMN11244975 |
| SRA |
SRX5565463 |
