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Sample GSM5956518 Query DataSets for GSM5956518
Status Public on Apr 03, 2022
Title A
Sample type SRA
 
Source name WT_CD11blow_12wk
Organism Mus musculus
Characteristics cell type: Mouse Alveolar macrophage (CD45+ Ly6G-SIglecF+ CD11c+)
age: 12 wks
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_12wk
WT_lo_12wk.narrowPeak.gz
WT_lo_12wk.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 SAMN26724481
SRA SRX14474345

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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