|
| Status |
Public on Jun 01, 2024 |
| Title |
TCL1, Tbx21-WT, replicate 1, scATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Eµ-TCL1 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E{mu}-TCL1 cells
genotype: Tbx21-WT
tissue: Spleen
strain: NSG
|
| Growth protocol |
Tbx21-KO (-/-) and Tbx21-WT (+/+) TCL1 cells were expanded in immunodeficient NSG animals.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mice were euthanized by increasing concentrations of carbon dioxide (CO2). Single-cell suspensions from spleens were prepared using the GentleMacs system. Splenocytes were enriched in TCL1 cells using EasySep™ Mouse Pan-B Cell Isolation Kit for further analyses, resulting in a purity above 97% of CD5+ CD19+ cells.
Libraries were prepared according to the Chromium single-cell ATAC v1.1 protocol (10x Genomics) using an in-house loaded Tn5.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
TCL1_Tbx21WT_260
|
| Data processing |
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.0.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: mm10-2020-A
Supplementary files format and content: pseudo-bulk bam, h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file
|
| |
|
| Submission date |
Jun 06, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Isabelle Seufert |
| Organization name |
DKFZ
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE234224 |
NF-κB-induced expression of T-bet suppresses proliferation of malignant B cells and is associated with good prognosis in chronic lymphocytic leukemia [scATAC-seq] |
| GSE234226 |
NF-κB-induced expression of T-bet suppresses proliferation of malignant B cells and is associated with good prognosis in chronic lymphocytic leukemia |
|
| Relations |
| BioSample |
SAMN35639459 |
| SRA |
SRX20599713 |
