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Sample GSM2871902 Query DataSets for GSM2871902
Status Public on Sep 28, 2018
Title H3K4me3 1
Sample type SRA
Source name HAP1
Organism Homo sapiens
Characteristics cell line: HAP1
treatment: None
chip-antibody: Rabbit anti-histone H3 trimethyl K4 (39159; Active Motif)
Treatment protocol For amino acid and serum starvation, cells were cultured for 3h in Earle's Balanced Salt Solution (EBSS; Life Technologies).
Growth protocol Cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin, 100 mg/ml streptomycin, and 10% heat-inactivated fetal calf serum (all obtained from Life Technologies) at 37 °C in 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells from two independent biological replicates were crosslinked in 1% formaldehyde, 5 mM Hepes-KOH (pH 7.5), 10 mM NaCl, 0.1 mM EDTA, and 50 µM EGTA and after 10 min crosslinking was stopped by adding 0.1 M glycine. Nuclei were isolated in 50 mM Tris (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, and 1% Triton X-100 and lysed in 20 mM Tris (pH 7.5), 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.3% SDS. Lysates were reduspended in 20 mM Tris (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1% X-100 and sonicated using Covaris (8 min, maximum output). Sheared DNA was incubated overnight with the indicated antibodies pre-coupled to protein A/G magnetic beads. Cells were washed and crosslinking was reversed by adding 1% SDS, 100 mM NaHCO3, 200 mM NaCl, and 300 mg/ml proteinase K. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research).
Endrepair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified and barcoded libraries were sequenced 75 bp single-end on Illumina NextSeq500 sequencer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Peaks were called using Cisgenome 2.0 (–e 150 -maxgap 200 –minlen 200).
Peak coordinates were stretched to at least 2000 base pairs and collapsed into a single list. Overlapping peaks were merged based on their outmost coordinates.
Only peaks identified by at least 2 independent datasets were further analyzed.
Peaks with differential H3K27ac, H3K56ac or H3K4me3 occupancy were identified using DESeq (padj<0.05) (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Cod file, containing peak coordinates
Submission date Dec 01, 2017
Last update date May 15, 2019
Contact name Janneke Peeters
Organization name UMC Utrecht
Street address Heidelberglaan 100
City Utrecht
ZIP/Postal code 3584CX
Country Netherlands
Platform ID GPL18573
Series (2)
GSE107599 Epigenetic profiling of human HAP1 cells before and after nutrient deprivation
GSE107603 Human HAP1 cells before and after nutrient deprivation
BioSample SAMN08118535
SRA SRX3436841

Supplementary file Size Download File type/resource
GSM2871902_H3K4Par1_dedup.unique_peak.cod.gz 681.2 Kb (ftp)(http) COD
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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