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Sample GSM4548600 Query DataSets for GSM4548600
Status Public on May 12, 2020
Title Microarray genotyping [1062201.3]
Sample type genomic
 
Source name human coronary artery smooth muscle cells
Organism Homo sapiens
Characteristics cell type: Coronary artery smooth muscle cells
passage: passage 4-7
Treatment protocol Not applicable
Growth protocol Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.
Label not applicable
Label protocol 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
 
Hybridization protocol RA1 resuspended DNA was loaded onto BeadChips arrays and incubate at 48C for overnight.
Scan protocol After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).
Description Sample 11
processed data file: SNP_table_9-15.txt
processed data file: Sample_9-15.txt
raw data file: Full_data_9-15.txt
raw data file: Paired_sample_table_9-15.txt
Data processing Genomic DNA extracted from human coronary artery smooth muscle cells was genotyped using Illumina Infinium Multi-Ethnic Global 8 Kit.
 
Submission date May 12, 2020
Last update date May 12, 2020
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 GPL24127
Series (2)
GSE141752 Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci
GSE150403 Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci [array]

Supplementary data files not provided
Processed data are available on Series record

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