|
| Status |
Public on Feb 05, 2025 |
| Title |
BM_ctrl_rep2_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell type: Hematopoietic progenitors
genotype: WT C57BL/6J
treatment: control
|
| Treatment protocol |
Tumor: mice were subcutaneously injected with PyMT-B6 cancer cell line. Ctrl: PBS was injected instead of cancer cells. Samples were collected 29 days (BM_ctrl_rep1, BM_tumor_rep1) or 21 days (all other samples) after injection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
BM samples: Lin- cells were sorted. Spleen samples: Lin-Kit+ and Lin-Kit+Sca+ cells were sorted and combined at a ratio of 1:1.
Nuclei were isolated following the 10x protocol CG000365 • Rev B. Isolated nuclei were further processed using the 10x “Single Cell Multiome ATAC + Gene Expression” platform (CG000338 Rev B).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data were processed using the "count" function of cellranger-arc (v2.0)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene-by-cell expression matrices and peak-by-cell chromatin accessibility matrices
Supplementary files format and content: fragments.tsv.gz: ATAC fragments
Supplementary files format and content: .arrow: arrow files created by ArchR
Library strategy: single cell multiome ATAC + GEX
|
| |
|
| Submission date |
Aug 05, 2024 |
| Last update date |
Feb 05, 2025 |
| Contact name |
Changxu Fan |
| E-mail(s) |
fanc@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue, Room 5213
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE274040 |
Transcriptional and chromatin accessibility landscapes of hematopoiesis in a mouse model of breast cancer |
|
| Relations |
| BioSample |
SAMN43041190 |
| SRA |
SRX25609624 |
