NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5723325 Query DataSets for GSM5723325
Status Public on Dec 08, 2021
Title Young HSC 0hour
Sample type SRA
 
Source name 10 week hematopoietic stem cells
Organism Mus musculus
Characteristics cell type: Murine bone marrow derived HSCs
surface markers: IL-7- Lin- Sca-1+ c-kit+ CD34- CD150+ CD48- Flt3-
age: 10-week-old
strain: C57BL/6
treatment: before cytokine stimulation
Treatment protocol cytokines stimulation:(SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11) LPS and polyIpolyC treatment : 10 μg LPS (InvivoGen) and 125 μg pIpC (InvivoGen) or PBS
Extracted molecule genomic DNA
Extraction protocol Transposase reaction was performed using nuclei prepared from freshly sorted 20,000 cells of each fraction
Libraries were then generated using a NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA). Library DNA was size-selected (240 - 360 bps) with BluePippin (Sage Science, Beverly, MA, USA). Sequencing was performed using HiSeq1500 (Illumina) with a single-read sequencing length of 60 bp.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Description Young HSC before cytokine stimulation
Data processing Sequences were aligned to mouse genome sequences (mm10) with Bowtie2(default setting) .
Mapped reads are subsampled with samtools to make numbers of reads same in all samples.
Macs2(ver2.2.6) was used to call peaks with nomodel, narrow peak option. With a q-value cutoff of 0.001
For visualization to make bigwig files,we used bamCoverage of deeptools with option " --binSize 20 --normalizeUsing CPM --smoothLength 60"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
 
Submission date Dec 08, 2021
Last update date Dec 09, 2021
Contact name Atsushi Iwama
Organization name The Institute of Medical Science, The University of Tokyo
Department Center for Stem Cell Biology and Regenerative Medicine
Lab Division of Stem Cell and Molecular Medicine
Street address 4-6-1, Shirokanedai
City Minato-ku
State/province Tokyo
ZIP/Postal code 108-8639
Country Japan
 
Platform ID GPL18480
Series (2)
GSE162662 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells
GSE190419 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells(ATAC-seq in cytokine and LPS:polyIpolyC experiments))
Relations
BioSample SAMN23771486
SRA SRX13351084

Supplementary file Size Download File type/resource
GSM5723325_Y_ATAC.bw 138.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap