|
| Status |
Public on Jul 08, 2024 |
| Title |
day9_KO_rep3_5FU - ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell type: Hematopoietic stem and progenitor cells (HSPCs)
genotype: Baf155 cKO (Vav-cre)
treatment: 5-FU (day9 post treatment)
|
| Treatment protocol |
Mice were injected i.p. with one dose of 5-FU (Sigma, Cat#: F6627) in PBS (150 mg/kg or 250 mg/kg body weight). Cells were sorted from BM 9 or 11 days post 5-FU treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
LK and LSK cells were FACS-sorted from the bone marrow 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
Library strategy: single cell multiome (ATAC)
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Jul 08, 2024 |
| 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 (2) |
| GSE240583 |
Baf155 establishes chromatin priming to promote hematopoietic regeneration and function [single cell multiome - ATAC + GEX] |
| GSE240585 |
Baf155 controls hematopoietic differentiation and regeneration through chromatin priming |
|
| Relations |
| BioSample |
SAMN36942339 |
| SRA |
SRX21334967 |
