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Sample GSM5723335 Query DataSets for GSM5723335
Status Public on Dec 08, 2021
Title Aged HSC H3K4me1
Sample type SRA
 
Source name 20 month 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: 20-month-old
strain: C57BL/6
antibody: H3K4me1
Treatment protocol Aged HSCs were stimulated with a mixture of cytokines (SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11) (BioLegend) in S-Clone SF-O3 (Sanko Junyaku) supplemented with 10% FBS, 50 μM 2-ME, and 1% GPS
Extracted molecule genomic DNA
Extraction protocol After FACSsorting, we used CUT&Tag-IT™ Assay Kit (Active motif). Anti-H3K27ac (Cat.8173, Cell signaling),Anti-H3K4me1(Cat.39498,Active motif) were used.
We used CUT&Tag-IT™ Assay Kit (Active motif) to library construction
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Data processing Library strategy: CUT&Tag
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
GSE190420 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (CUT&TAG H3K27ac,H3K4me1)
Relations
BioSample SAMN23771500
SRA SRX13351094

Supplementary file Size Download File type/resource
GSM5723335_A_K4me1.bw 210.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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