|
| Status |
Public on Dec 08, 2021 |
| Title |
Young HSC LPS sample2 |
| Sample type |
SRA |
| |
|
| Source name |
hematopoietic stem cells treated with LPS
|
| 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: LPS treatment
|
| 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 HSCs after LPS treatment and 4week interval
|
| 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 |
SAMN23771493 |
| SRA |
SRX13351091 |
