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| Status |
Public on Jul 06, 2016 |
| Title |
Athero_Artery_ATAC_D5 |
| Sample type |
SRA |
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| Source name |
Human coronary artery explant tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue state: Atherosclerotic coronary artery (media)
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| Treatment protocol |
Atherosclerotic diseased coronary arteries were dissected from a diseased explanted donor heart and media was carefully separated before snap freezing.
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| Growth protocol |
N/A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
10-20 mg of pulverized fresh frozen tissue was suspended in 1 mL 1x PBS and centrifuged at 2,000 x g for 3 min at 4° C. The pellet was resuspended in 1 mL of a lysis buffer containing 50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100 and supplemented with an EDTA-free complete protease inhibitor (Roche). This suspension was incubated at 4° C for 10 minutes and then dounce homogenized. The homogenate was centrifuged at 2,000 x g for 5 min at 4° C, and the resultant pellet was resuspended in 1 mL 1x PBS. Cellular debris was filtered with a cell strainer, and intact nuclei were quantified. 5x10^4 nuclei were subjected to Tn5 mediated transposition for 1 hour and tagmented DNA was purified as previously reported.
Libraries were PCR amplified and purified as described previously and were subjected to an additional electrophoresis step on an E-Gel EX 2% agarose gel (Invitrogen), and gel fragments correlating to 100-1000 bp were excised and purified. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, 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 |
SAMN04075625 |
| SRA |
SRX1235299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1876033_19Athero_L2_TAAGGCGA_L002_peaks.bed.gz |
499.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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