|
| Status |
Public on Nov 20, 2023 |
| Title |
Jurkat_DMSO_GATA3 |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T-ALL
treatment: DMSO
antibody: GATA3
|
| Treatment protocol |
The cells were incubated with CUTANA pA/G-Mnase. Chromtin fragments were purified utilizing a Cutana DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and analyzed on Illumina Novaseq at GENEWIZ Azenta Life Sciences Co. Ltd.
|
| Growth protocol |
TAL1-FKBP12 Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction from the Cut&Run-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 Cut&Run-Seq sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CUT&RUN-seq data were preprocessed and analyzed using cutRunTools pipeline.
This pipeline automated the preprocessing and alignment of CUT&RUN-seq data to hg19 genome. CutRunTools utilized MACS2 and SEACR software to call peaks using the default optimized cutoff for each CUT&RUN-seq data.
The paired control data was further utilized by the cutRunTools step2 script to normalize the MACS2 output peaks.
Each bedGraph output has been further normalized by subtracting the treatment file to the corresponding control file using MACS2 bdgcmp and floored the signal to 0.1 before convert to bigWig using UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Peak bed files of GATA3 and RUNX1
Supplementary files format and content: bigWig files of GATA3 and RUNX1
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Feb 23, 2023 |
| Last update date |
Nov 20, 2023 |
| 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) |
| GSE225936 |
Cut&Run analysis for transcription factors in TAL1-FKBP12 Jurkat cells |
| GSE225941 |
Regulatory mechanisms and context-dependent roles of TAL1 in TALL |
|
| Relations |
| BioSample |
SAMN33424355 |
| SRA |
SRX19484292 |
