|
| Status |
Public on Dec 08, 2021 |
| Title |
Young HSC H3K4me1 |
| 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
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 |
SAMN23771498 |
| SRA |
SRX13351092 |
