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Status |
Public on Jul 06, 2016 |
Title |
HCASMC_ChIP_H3K27ac_D2 |
Sample type |
SRA |
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Source name |
HCASMC Cell Applications 2989
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Organism |
Homo sapiens |
Characteristics |
cell treatment: Normal serum chip antibody: H3K27ac, Abcam ab4729
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Treatment protocol |
N/A
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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).
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
Sep 13, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Thomas Quertermous |
E-mail(s) |
tomq1@stanford.edu
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Phone |
650-723-5012
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Organization name |
Stanford University
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Department |
Medicine Cardiology
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Lab |
Quertermous
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Street address |
300 Pasteur Drive
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City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
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Platform ID |
GPL16791 |
Series (1) |
GSE72696 |
Integrative fine-mapping of regulatory variants and mechanisms at coronary artery disease loci |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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