|
| Status |
Public on May 12, 2020 |
| Title |
Microarray genotyping [9102101] |
| 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 12
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] |
|
