|
| Status |
Public on Dec 05, 2020 |
| Title |
young MPP2 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
10 week multipotent progenitor 2s
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow derived MPP2s
surface markers: IL-7- Lin- Sca-1+ c-kit+ CD34+ CD150+ CD48+ Flt3-
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 |
|
| Relations |
| BioSample |
SAMN16982947 |
| SRA |
SRX9621047 |
