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| Status |
Public on Sep 29, 2016 |
| Title |
H3K4me3ChIPseq_2 |
| Sample type |
SRA |
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| Source name |
in vitro transformed human skin fibroblasts
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| Organism |
Homo sapiens |
| Characteristics |
cell type: in vitro transformed human skin fibroblasts
chip antibody: anti-H3K4me3 (ab8580, Abcam)
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| Growth protocol |
Cells were grown in minimum essential medium (MEM) containing 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, at 37 °C in 5% CO2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested with trypsin and ChIP was performed as previously described (Sailaja et al., Methods in molecular biology, 2012).
Library construction was carried out as published (Blecher-Gonen et al., 2013, Nat Prot). Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ChIP-seq
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| Data processing |
Raw reads that passed the quality controls were aligned to human genome assembly hg19 using Bowtie 0.12.7 (Langmead et al. Genome Biol., 2009), taking only uniquely aligned reads with no more than 2 mismatches.
Significant peaks of H3K4me3 and H3K27me3 were extracted using MACS 1.4 (Zhang et al., 2008), using a minimal p-value cutoff of 10E-5 and a fold change for model building of 30.
Peak detection for H1.0 and H1.4 was performed using in house scripts. In short, reads were counted within 50 bp windows. The median was calculated for each three bins and normalized by the sum of the reads. To effectively capture local biases in the genome, the Log2 ratio between the ChIP samples and the input genomic DNA was calculated. Peaks were defined as regions with log2 ratio of ChIP DNA over Input DNA > 2 within six neighbouring windows, and average number of reads > 15.
Genome_build: hg19
Supplementary_files_format_and_content: bed format
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| Submission date |
Feb 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Eran Meshorer |
| E-mail(s) |
meshorer@huji.ac.il
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| Organization name |
The Hebrew University of Jerusalem
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| Department |
Genetics
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| Street address |
Edmond J. Safra Campus
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| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE66169 |
The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity |
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| Relations |
| BioSample |
SAMN03360793 |
| SRA |
SRX885223 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1615881_H3K4_2_Peaks.bed.gz |
241.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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