|
| Status |
Public on Jul 02, 2024 |
| Title |
DND41_ACBI-24H2_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DND41-cells
atac antibody: ATAC
|
| Treatment protocol |
The cells are incubated with Tn5 transposase. Tagmented DNA fragments are purified with Zymo DNA purification kit. ATAC libraries are purified and sequenced on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.
|
| Growth protocol |
DND-41 and MOLT-4 were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep with 100nM ACBI-1 or DMSO.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction from the ATAC-seq samples and sequencing of paired-end 150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end ATAC-Seq sequencing
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ATAC-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ATAC-seq reads were remove duplicate with Picard MarkDuplicates package. Multiple mapping reads were removed using samtools view -q 10
ATAC-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is p-value < 1e-5, keep-dup=all, --SPMR were used to normalized the bedGraph output.The signal has been floored to 0.1 after bdgcmp subtract function.
Assembly: hg19
Supplementary files format and content: narrowPeak files of ATAC-seq
Supplementary files format and content: bigWig files of ATAC-seq
|
| |
|
| Submission date |
Apr 25, 2023 |
| Last update date |
Jul 02, 2024 |
| Contact name |
Tze King Tan |
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute
|
| Lab |
Takaomi Sanda Lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE230584 |
ATAC-seq analysis for DND-41 and MOLT4 cells with ACBI-1 treatment |
| GSE230594 |
Oncogenic roles of SWI/SNF chromatin remodeling factors: therapeutic targets in T-cell acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN34370342 |
| SRA |
SRX20097803 |
