|
| Status |
Public on Mar 13, 2023 |
| Title |
GMP-MoP, bio rep 1 [ATAc-seq] |
| Sample type |
SRA |
| |
|
| Source name |
BM
|
| Organism |
Mus musculus |
| Characteristics |
tissue: BM
cell type: BM progenitor cells
sample group: GMP-MoP
antibodies/tags: Illumina Tagment DNA Enzyme
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Five thousand progenitor cells were sorted into 1.5 mL tubes. Transposition reaction was performed by using Tagment DNA Enzyme and Buffer Kit (Illumina).
Sequence libraries wre prepared by PCR-amplification of the transposed genomic DNA (New England Biolabs) with indexed primers.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were aligned to a mousereference genome in the Bowtie2 (version 2.3.5.1).
ATAC-seq data for GMP and MDP were retrieved from NCBI/GEO (GSE149762).
Peak identification and calculation of read counts per peak were performed using the HOMER software (version 4.11).
A catalog file of peak data was created and read count values were calculated by using the HOMER software.
The R package edgeR (version 3.32.1) was used for normalization of read counts and calculation of RPKM values for each peak.
Assembly: mm10
Supplementary files format and content: BED files include ATAC-seq peak regions and raw count values.かんがえる
|
| |
|
| Submission date |
Jan 31, 2023 |
| Last update date |
Mar 13, 2023 |
| Contact name |
Kenichi Asano |
| E-mail(s) |
asanok@toyaku.ac.jp
|
| Organization name |
Tokyo University of Pharmacy and Life Sciences
|
| Department |
Life Sciences
|
| Lab |
Immune Regulation
|
| Street address |
1432-1 Horinouchi
|
| City |
Hachioji |
| State/province |
Tokyo |
| ZIP/Postal code |
1920392 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE224100 |
The chromatin structures of GMP-MoPs are shifted toward ones that favors an aberrant differentiation pathway generating GMP-MoPs from proNeu1 [ATAC-seq] |
| GSE224702 |
mouse RNA-seq, human RNA-seq, ATAC-seq, and scRNA-seq analyses data |
|
| Relations |
| BioSample |
SAMN32971684 |
| SRA |
SRX19226821 |
