|
| Status |
Public on Dec 08, 2021 |
| Title |
Young HSC |
| 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
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After FACS sorting and purification of HCSs, nuclei are isolated using Chromium Next GEM Single Cell ATAC Reagent Kits v1.1
Libraries were then generated using Chromium Next GEM Single Cell ATAC Reagent Kits v1.1
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Base call files were demultiplexed into fastq files by "cell ranger-atac mkfastq"
We used "cellranger-atac count" for Read alignment, barcode counting and peak calling
With "filtered_peak_bc_matrix.h5", "fragments.tsv.gz" and "singlecell.csv" generated from cellranger-atac, We used Signac to perform subsequent analysis
Genome_build: mm10
Supplementary_files_format_and_content: filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv
|
| |
|
| 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 |
| GSE190424 |
Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (single cell ATAC-seq) |
|
| Relations |
| BioSample |
SAMN23771536 |
| SRA |
SRX13351452 |
