|
| Status |
Public on Apr 10, 2024 |
| Title |
MLL_AF4_Rep1 (PDX_ATAC) |
| Sample type |
SRA |
| |
|
| Source name |
PDX
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PDX
disease state: B_ALL
disease subgroup: MLL_AF4
|
| Growth protocol |
RPMI 1640 + 10% serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fast-ATAC in fresh primary ALL cells from patients and in a subset of ALL cell lines (BALL1, CEM, Jurkat and P12-Ichikawa) was performed on 10,000 cells as described in (https://0-doi-org.brum.beds.ac.uk/10.1038/ng.3646) and (https://0-doi-org.brum.beds.ac.uk/10.1038/s41375-022-01685-z). Paired-end Illumina next-generation sequencing of Fast-ATAC libraries was performed at the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children’s Research Hospital. Data were analyzed as in (https://0-doi-org.brum.beds.ac.uk/10.1038/s41375-022-01685-z).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ATAC-seq on ALL patient derived xenografts (PDX_ATAC)
|
| Data processing |
Data were analyzed as in (https://0-doi-org.brum.beds.ac.uk/10.1038/s41375-022-01685-z), GSE161501, and GSE129066.
Assembly: HG19
Supplementary files format and content: .narrowpeak for accessible regions
|
| |
|
| Submission date |
Feb 21, 2023 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Daniel Savic |
| E-mail(s) |
daniel.savic@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pharmaceutical Sciences
|
| Lab |
Savic
|
| Street address |
262 Danny Thomas pl.
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE224204 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment |
| GSE224530 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN33398400 |
| SRA |
SRX19460460 |
