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Sample GSM7060669 Query DataSets for GSM7060669
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
BioSample SAMN33424327
SRA SRX19484298

Supplementary file Size Download File type/resource
GSM7060669_Jurkat_H3K27ac_dTAG.allValidPairs.txt.gz 4.2 Gb (ftp)(http) TXT
GSM7060669_Jurkat_H3K27ac_dTAG.anchors.bed.gz 560.5 Kb (ftp)(http) BED
GSM7060669_Jurkat_H3K27ac_dTAG.filt.intra.loop_counts.bedpe.gz 2.0 Mb (ftp)(http) BEDPE
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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