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Sample GSM1876037 Query DataSets for GSM1876037
Status Public on Jul 06, 2016
Title HCASMC_ChIP_H3K27ac_D2
Sample type SRA
 
Source name HCASMC Cell Applications 2989
Organism Homo sapiens
Characteristics cell treatment: Normal serum
chip antibody: H3K27ac, Abcam ab4729
Treatment protocol N/A
Growth protocol Human coronary artery smooth muscle cells were obtained from Cell Applications, and media was purchased from Lonza. Cells were maintained as suggested in SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and 5% FBS, but without antibiotics (Lonza, #CC-3182).
Extracted molecule genomic DNA
Extraction protocol 1x10^7 HCASMC per condition were crosslinked for 10 min with 1% formaldehyde, followed by quenching with glycine. Cells were lysed for 10 min on ice, and nuclei were then lysed for 10 min on ice. Crosslinked chromatin was sheared to 100-500bp fragments by sonication for 3x5 min using a Bioruptor Pico sonicator (Diagenode). 5 ug IgG or H3K27ac (Abcam ab4729) antibody was incubated with diluted chromatin overnight at 4C, and ChIP DNA was receoved as previously described.
Libraries were generated by ligating ChIP DNA with Illumina TruSeq adapters, followed by PCR amplification and gel electrophoresis. ChIP DNA library fragments around 300bp were selected for PCR amplification and libraries were quantitated using Qubit fluorometric and bioanalyzer analyses.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Alignment
ATAC-seq and ChIP-seq reads in raw fastq files were aligned to hg19 using bowtie2 set to default parameters. RNA-seq reads were aligned to hg19 using the RNA-seq aligner STAR (v2.4.0i).
These ChIPseqs were done on a different machine as paired ends, no replicates, sequences combined in a bam file which was used to create the bed file provided, otherwise handled as noted for the other ChIPseqs.
Peak-calling
ATAC-seq and ChIP-seq peaks were called with MACS1.4 for hg19, set to default parameters using IgG samples as a background control.
Feature counts
ATAC-seq mapped reads were counted using the HOMER annotatePeaks script after normalization of reads. RNA-seq mapped reads were counted using the featurecounts script distributed with the Rsubread package, and differential expression of exons, genes, and transcripts were assayed using the DESeq2 R package from Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files standard format
Supplementary_files_format_and_content: RNA-Seq proccesed files (featureCounts): one for gene and one for transcript IDs
Supplementary_files_format_and_content: .csv DESeq output files
 
Submission date Sep 13, 2015
Last update date May 15, 2019
Contact name Thomas Quertermous
E-mail(s) tomq1@stanford.edu
Phone 650-723-5012
Organization name Stanford University
Department Medicine Cardiology
Lab Quertermous
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16791
Series (1)
GSE72696 Integrative fine-mapping of regulatory variants and mechanisms at coronary artery disease loci
Relations
BioSample SAMN04075628
SRA SRX1235303

Supplementary file Size Download File type/resource
GSM1876037_CA2989_H3K27ac_CGATGT_peaks.bed.gz 936.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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