GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4954108 Query DataSets for GSM4954108
Status Public on Dec 05, 2020
Title young CLP rep1
Sample type SRA
Source name 10 week common lymphoid progenitor
Organism Mus musculus
Characteristics cell type: Murine bone marrow derived CLPs
surface markers: IL-7+ Lin- Sca-1 low c-kit low
age: 10-week-old
strain: C57BL/6
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
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,reads per million mapped read (RPM) values of the sequenced reads were calculated every 200-base pair bin with a shifting size of 100 base pairs using bed tools and normalized with the amount of ChIP DNA in the H3K27me3 analysis.
Genome_build: mm10
Submission date Dec 02, 2020
Last update date Dec 06, 2020
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)
GSE162551 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells(ATAC-seq)
GSE162662 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells
BioSample SAMN16982968
SRA SRX9621056

Supplementary file Size Download File type/resource 114.9 Mb (ftp)(http) BW
GSM4954108_27_Y-CLP_1_peaks.narrowPeak.gz 882.2 Kb (ftp)(http) NARROWPEAK
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