|
Status |
Public on Apr 10, 2024 |
Title |
TALL_Rep1 (PDX_ATAC) |
Sample type |
SRA |
|
|
Source name |
PDX
|
Organism |
Homo sapiens |
Characteristics |
cell type: PDX disease state: T_ALL disease subgroup: NA
|
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 |
SAMN33398402 |
SRA |
SRX19460458 |