GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM721136 Query DataSets for GSM721136
Status Public on Sep 16, 2011
Title HCC1954: chromatin IP against H3K27ac
Sample type SRA
Source name breast cancer cells
Organism Homo sapiens
Characteristics cell line: HCC1954
cell type: breast cancer cells
chip antibody: H3K27ac, cat #39133, lot #19208002
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 H3K27ac
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)
SRA SRX061991
BioSample SAMN00264830

Supplementary file Size Download File type/resource
GSM721136_HCC1954.merged.H3K27ac.nodup.bam 727.1 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap