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| Status |
Public on Sep 28, 2018 |
| Title |
H3K4me3 1 |
| Sample type |
SRA |
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| Source name |
HAP1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HAP1
treatment: None
chip-antibody: Rabbit anti-histone H3 trimethyl K4 (39159; Active Motif)
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| Treatment protocol |
For amino acid and serum starvation, cells were cultured for 3h in Earle's Balanced Salt Solution (EBSS; Life Technologies).
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| 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.
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| 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.
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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 |
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
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| Submission date |
Dec 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Janneke Peeters |
| E-mail(s) |
j.g.c.peeters-7@umcutrecht.nl
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| Organization name |
UMC Utrecht
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| Street address |
Heidelberglaan 100
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| City |
Utrecht |
| ZIP/Postal code |
3584CX |
| Country |
Netherlands |
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| 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 |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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