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Sample GSM721138 Query DataSets for GSM721138
Status Public on Sep 16, 2011
Title HCC1954: chromatin IP against H3K36me3
Sample type SRA
 
Source name breast cancer cells
Organism Homo sapiens
Characteristics cell line: HCC1954
cell type: breast cancer cells
chip antibody: H3K36me3, cat #ab9050-100, lot #707946
Extracted molecule genomic DNA
Extraction protocol To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Branson 450 Sonifier (Branson, Danbury, CT). Following ChIP performed with Dynal beads (Invitrogen, Carlsbad, CA), ChIP DNA was subjected to end repair, A-tailing, adaptor ligation, and gel purification. Following PCR amplification for 18 cycles, the final library underwent gel purification.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description H3K36me3
Instrument models: both Illumina Genome Analyzer IIx and Illumina HiSeq 2000 were used.
Data processing We mapped ChIP-Seq reads using the Bowtie program, keeping only those reads that mapped uniquely to hg18 with at most 3 mismatches. Specifically, the parameters used were: "--solexa1.3-quals -v 3 -m 1 --best --strata -S ". PCR duplicates for each library were removed with the Picard program(Picard 2011). All biological replicates were combined and compressed/indexed by the SAMtools suite into BAM format(Li et al. 2009).
Genome build: hg18
 
Submission date May 06, 2011
Last update date May 15, 2019
Contact name Gary Chung Hon
Organization name UT Southwestern
Department OB/GYN
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platform ID GPL10999
Series (2)
GSE29069 Global DNA Hypomethylation Coupled to Repressive Chromatin Domain Formation and Gene Silencing in Breast Cancer
GSE29118 Genome-wide location analysis in breast cancer cells (HCC1954)
Relations
SRA SRX061994
SRA SRX061995
BioSample SAMN00264832

Supplementary file Size Download File type/resource
GSM721138_HCC1954.merged.H3K36me3.nodup.bam 4.2 Gb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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