|
| Status |
Public on Nov 24, 2019 |
| Title |
Blood_CAD_D0 [hyb20759] |
| Sample type |
RNA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
patient diagnosis: CAD
time point: D0
|
| Growth protocol |
Whole blood RNA from peripheral blood of patients.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using PAXgene Blood miRNA kit, followed by ethanol purification.
|
| Label |
biotin
|
| Label protocol |
100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChipTM WT PLUS Reagent Kit for GeneChipTM Whole Transcript Expression Arrays
|
| |
|
| Hybridization protocol |
A mixture of purified and fragmented biotinylated cDNA and hybridization controls (Affymetrix) was hybridized (16 hours at 45°C) on Affymetrix HTA 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s instructions.
|
| Scan protocol |
Chips were scanned using a GeneChip® scanner 3000 (Affymetrix)
|
| Data processing |
Raw data was preprocessed on the Affymetrix Expression Console 1.4.1.46 and normalized using Robust Multi-Array Average and Signal Space Transformation. Inter-array variability was adjusted by fitting a linear model. The normalized data was downstream analyzed using Bioconductor 3.1 for R version 3.2.2 3. A linear model was fit using the package limma 3.24.15 to determine differential expression between MI at the 2 different time points and stable controls.
|
| |
|
| Submission date |
Dec 04, 2018 |
| Last update date |
Nov 26, 2019 |
| Contact name |
Maarten Vanhaverbeke |
| E-mail(s) |
[email protected]
|
| Organization name |
KU Leuven
|
| Department |
Cardiovascular Sciences
|
| Street address |
Herestraat 49 box 911
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE123342 |
Peripheral blood whole transcriptome in patients with acute myocardial infarction and at follow-up |
|
