|
| Status |
Public on Apr 03, 2022 |
| Title |
H |
| Sample type |
SRA |
| |
|
| Source name |
WT_CD11blow_4wk
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse Alveolar macrophage (CD45+ Ly6G-SIglecF+ CD11c+)
age: 4wks
genotype: WT (C57BL/6)
|
| Treatment protocol |
Cells were sorted into RPMI1640 + 20% heat-inactivated FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase followed by
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
WT_CD11blow_4wk
WT_lo_4wk.narrowPeak.gz
WT_lo_4wk.fc.signal.bigwig
|
| Data processing |
Sequencing reads were demultiplexed and aligned to human 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)
Assembly: hg19
Supplementary files format and content: bigwig, narrowPeak
|
| |
|
| Submission date |
Mar 16, 2022 |
| Last update date |
Apr 03, 2022 |
| Contact name |
Mary C Dinauer |
| E-mail(s) |
mdinauer@wustl.edu
|
| Organization name |
Washington University In St Louis
|
| Department |
Pathology & Immunology
|
| Street address |
660 South Euclid Ave
|
| City |
St Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE198768 |
Genome-wide epigenome mapping in alveolar macrophages (CD45+ Siclec F+ CD11c+) from WT (4wks and 12 wks) and CGD (4wks and 12 wks) mice |
| GSE198778 |
The leukocyte NADPH oxidase 2 (NOX2) plays a key role in pathogen killing and immunoregulation |
|
| Relations |
| BioSample |
SAMN26724474 |
| SRA |
SRX14474352 |
