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Sample GSM4108013 Query DataSets for GSM4108013
Status Public on Aug 20, 2020
Title BA_P7_48+LSK_U3 ATAC-seq
Sample type SRA
 
Source name Hematopoietic progenitor cell
Organism Mus musculus
Characteristics age: P7
genotype: Wildtype
cell type: Hematopoietic progenitor 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 U3
Processed data file: BA_P7_48+LSK.fc.signal.bigwig
Processed data file: BA_P7_48+LSK.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 SAMN12912803

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

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