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| Status |
Public on Jul 06, 2016 |
| Title |
HCASMC_ATAC_PDGFDD_D1 |
| Sample type |
SRA |
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| Source name |
HCASMC Cell Applications 020805.2
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| Organism |
Homo sapiens |
| Characteristics |
cell treatment: PDGF-DD
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| Treatment protocol |
Cells were maintained in normal media until 70% confluence and media was changed to serum-free without supplements for 18h and cells were stimulated with growth factors for 6 hours in serum-free, supplement-free media.
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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 |
5x10^4 fresh HCASMC were collected by centrifugation and and nuclei extracted with cold lysis buffer containting 10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL and nuclei were resuspended in transposition reaction buffer containing Tn5 transposases (Illumina Nextera). Transposition reactions were incubated at 37C for 30 minutes, followed by DNA purification using Zymo DNA Clean-up and Concentration Kit.
Libraries were PCR amplified and purified as described previously. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity and TBE gel electrophoresis, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed. Libraries were quantitated using Qubit high sensitivity DNA reagent, and quantitative PCR (KAPA Biosystems).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Library strategy: ATAC-seq
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 |
SAMN04075614 |
| SRA |
SRX1235290 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1876024_020805.2_L1_AGGCAGAA_L001_peaks.bed.gz |
2.5 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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