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Sample GSM425485 Query DataSets for GSM425485
Status Public on Jul 08, 2009
Title H3K36me3_ChIPSeq
Sample type SRA
Source name MDA-MB-231 cells
Organism Homo sapiens
Characteristics cell type: Human breast adenocarcinoma cell line
Growth protocol MDA-MB-231 cells were grown in DMEM containing 15% FBS, L-glutamine, non-essential amino acids, and penicillin/streptomycin.
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation was performed with rabbit anti-trimethyl histone H3K36 (Abcam, ab32356) and rabbit anti-dimethyl histone H3K4 (Abcam, ab9050) according to previously described methods (Steger et al. 2008). Following elution, IP samples were treated with RNaseA at 65ºC overnight followed by proteinase K at 42ºC for 2 hours. DNA was isolated by phenol:chloroform extraction and ethanol precipitation. ChIP DNA was prepared for Illumina sequencing according to the protocol described by Robertson et al (Robertson et al. 2007) and the manufacturer's recommendations.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Description Chromatin IP against H3K36me3
Data processing Alignment: Sequence reads from ChIP-seq experiments were mapped to the human genome (March 2006) with the RMAP program, allowing at most 2 mismatches in 36 bases. Reads mapped ambiguously to multiple locations in the genome were ignored in subsequent analysis.
Submission date Jul 08, 2009
Last update date May 15, 2019
Contact name Emily Hodges
Organization name Cold Spring Harbor Laboratory
Street address 1 Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platform ID GPL9115
Series (1)
GSE17001 High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
SRA SRX007142
BioSample SAMN02198686
Named Annotation GSM425485_MB231_H3K36_aligned.bed.gz

Supplementary file Size Download File type/resource
GSM425485_MB231_H3K36_aligned.bed.gz 365.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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