|
| Status |
Public on Nov 20, 2023 |
| Title |
Jurkat_dTAG_H3K27ac_Hi-CHIP |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T-ALL
treatment: dTAG
chip antibody: H3K27ac Antibody (Abcam; ab4729)
|
| Treatment protocol |
The cells were cross-linked with formaldehyde, lysed with Hi-C buffer, and then sonicated. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. Post-ChIP DNA was tagmented with Tn5 enzyme follwed by PCR amplification library synthesis.
|
| 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 H3K27ac Hi-ChIP-seq samples and sequencing of paired-end 100-bp-long reads by the DNBSEQ platform were performed at BGI Genomics.
Paired-end Hi-ChIP
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Hi-ChIP data were aligned and processed using HiC-Pro pipeline version 2.11.1, and the reads in the fastq files were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 version 2.4.1.
The restriction sites ^GATC and G^ANTC across the human genome were cut and utilized by HiC-Pro using the HiC-Pro Utilities Python script “digest genome”.
HiC-Pro configuration on ligation site were set to be ^GATC and G^ANTC optimize for ARIMA kit data. The aligned data were further processed using hichipper to call interactions.
Hichipper version 2.7.9 was used to extract the valid interactions from the HiC-Pro data and generate the bedpe interaction file by utilizing anchors from peaks called by MACS2 broadPeak using the dangling-end and self-cycle Hi-ChIP read pairs with the following parameters: --keep-dup all -p 1e-9 --extsize 147 --nomodel -f bed.
Hichipper used to process interactions using the following parameters: -l 50 -mi 5000 -ma 2000000.
Assembly: hg19
Supplementary files format and content: *_allValidPairs: txt file output from HiC-Pro
Supplementary files format and content: *.intra.loop_counts.bedpe: bedpe file output from hichipper
Supplementary files format and content: *.anchors.bed: anchor used by hichipper
Library strategy: Hi-ChIP
|
| |
|
| 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 |
GPL28038 |
| Series (2) |
| GSE225937 |
H3K27ac Hi-ChIP analysis in TAL1-FKBP12 Jurkat cells |
| GSE225941 |
Regulatory mechanisms and context-dependent roles of TAL1 in TALL |
|
| Relations |
| BioSample |
SAMN33424327 |
| SRA |
SRX19484298 |
