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| Status |
Public on Jun 05, 2020 |
| Title |
KPS_H3K27ac |
| Sample type |
SRA |
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| Source name |
KARPAS-45
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| Organism |
Homo sapiens |
| Characteristics |
cell type: T-ALL cell line
cell line: KARPAS-45
chip antibody: H3K27Ac (ab4729, Abcam)
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| Growth protocol |
T-ALL cell were cultured in RPMI-1640 medium supplemented with 10% (PER-117) or 20% FBS (KARPAS-45), 2mM L-glutamine and 100 U/ml penicillin G- streptomycin in 5% CO2 at 37°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
107 cells were cross-linked for each ChIP experiment with 1.1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. The purified chromatin was fragmented to 200–300 bp fragments by sonication (Covaris, Woburn, MA, USA; S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 μl of protein-A coated beads (Thermo-Scientific, Waltham, MA, USA; catalog number 53139) and 10 μg of the specified antibodies. The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65 °C overnight. DNA was subsequently purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime
DNA obtained from the ChIP assays was adaptor ligated, amplified and analyzed by Illumina sequencing
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw sequencing data were mapped to the human reference genome (hg38) using STAR v2.4.2a with --outFilterMultimapNmax 1 and --alignIntronMax 1
Peak calling was performed using MACS2 with default settings and using input DNA as control. For histone marks, --broad option was turned on
Genome_build: hg38
Supplementary_files_format_and_content: bed/narrowPeak MACS2 output containing histone marks/ RUNX2 peaks
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| Submission date |
Jun 04, 2020 |
| Last update date |
Jun 06, 2020 |
| Contact name |
Filip Matthijssens |
| E-mail(s) |
Filip.Matthijssens@UGent.be
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| Phone |
093325268
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| Organization name |
Ghent University
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| Department |
Biomolecular Medicine
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| Lab |
Lab of normal and malignant hematopoesis
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| Street address |
Corneel Heymanslaan 10
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| City |
Ghent |
| State/province |
België |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE151819 |
RUNX2 is a dependency factor in immature and KMT2A-rearranged T-cell acute lymphoblastic leukemia [RUNX2 ChIP-seq] |
| GSE151823 |
RUNX2 is a dependency factor in immature and KMT2A-rearranged T-cell acute lymphoblastic leukemia |
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| Relations |
| BioSample |
SAMN15102420 |
| SRA |
SRX8472390 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4591425_KRPS_H3K27ac.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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