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| Status |
Public on Aug 23, 2017 |
| Title |
CL0000_H3K9me3_MINUS_M32_REP_001 |
| Sample type |
SRA |
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| Source name |
H3K9me3 MINUS M30
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| Organism |
Homo sapiens |
| Characteristics |
cell type: immortalized human astrocytes
genotype: -dox (wild-type)
passage: 30
chip antibody: H3K9me3
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| Growth protocol |
Stable immortalized astrocytes were grown in DMEM + 10% FBS. Inducible astrocytes were grown in DMEM + Tetracycline-free FBS (10%) and IDH1 R132H expression was induced with the addition of 1 ug/ml of doxycycline. Tumorspheres were grown in NeuroCult NS-A Proliferation media (STEMCELL Technologies) with EGF and FGF.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using the Magna ChIP™ G - Chromatin Immunoprecipitation Kit (Millipore) according to manufacturer's instructions.
Libraries were prepared according to Illumina's instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CL0000_H3K9me3_MINUS_M32_REP_001
processed data file: H3K9me3_MINUS_M32.rpkm.bedgraph
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| Data processing |
Raw sequencing data were aligned to the hg37 genome build using the Burrows-Wheeler Aligner (BWA) version 0.7.10.
Further indel realignment, base-quality score recalibration and duplicate-read removal were performed using the Genome Analysis Toolkit (GATK) version 3.2.2 following raw reads alignments guidelines
To call enriched regions, we first applied Model-based Analysis of ChIP-Seq (MACS2 version 2.1.0) to all histone marks. For narrow histone marks (H3K4me) resulting raw peaks were filtered by by pval=0.01. Next, for each peak, RPKM (Reads Per Kilobase of transcript per Million mapped reads) was calculated for IP (immuno-precipitated) and INPUT bam files. Only those peaks with RPKM INPUT/RPKM IP ratio greater than 0.5 were reported to final result.
For broad histone marks (H3K36me3, H3K9me3, H3K27me3, H4K20me3) resulting raw peaks were filtered by by pval=0.1.
To ensure high stringency of broad peak calling, we applied the second peak caller called SICER version 1.1 following the instructions provided with download. Two sets of peaks were merged using bedtools merge tool, only intersecting broad peaks were reported.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files include peak coordinates and RPKM values for each sample.
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| Submission date |
Aug 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vladimir Makarov |
| E-mail(s) |
makarov@ccf.org
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| Organization name |
Cleveland Clinic
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| Department |
LRI
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| Lab |
CITI
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| Street address |
9500 Euclid Ave
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| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE85940 |
Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence [ChIP-seq] |
| GSE85942 |
Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence |
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| Relations |
| BioSample |
SAMN05607246 |
| SRA |
SRX2039775 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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