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Sample GSM3147770 Query DataSets for GSM3147770
Status Public on Jun 27, 2018
Title U2OS H3K4me3 ChIP-seq
Sample type SRA
Source name Osteosarcoma
Organism Homo sapiens
Characteristics cell line: U2OS
cell type: Cultured cancer cell line
chip antibody: H3K4me3 antibody (9751P, Cell Signaling)
Growth protocol Cancer cells were grown in DMEM medium, 10% FBS
Extracted molecule genomic DNA
Extraction protocol DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using each antibodies. Enriched DNA molecules were then amplified randam primer with klenow fragment and sequenced by Illumina Genome Analyzer IIx.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).
Illumina paired-end sequencing
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description ChipSeq for H3K4me3
Data processing For RepID ChIP, the MACS peak calling program was used comparing reads from the ChIP –seq experiment to genomic input reads from the same cell line, with default parameters, and a p-value = 1e-9.
For nascent strand peak calling the SICER program was used. Nascent strand reads were called by comparison to HCT116 genomic reads using a window size of 200bp, gap size of 600pb, and FDR of 0.00001. For ChiP sequencing peak calling, the SICER program was used except for H4K16Ac ChIP, which are called peaks by broad MACS. For peak calling, used same length sequenced genomic control (101bp or 125bp)
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq
Submission date May 21, 2018
Last update date Jun 27, 2018
Contact name Christophe E Redon
Phone 240-760-7338
Organization name NIH
Street address 37 Convent Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL9052
Series (1)
GSE114703 The Replication-initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin
BioSample SAMN09232387
SRA SRX4107937

Supplementary file Size Download File type/resource
GSM3147770_H3K4me3_PHIPWT.broadPeak.bed.gz 658.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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