|
| Status |
Public on Oct 29, 2013 |
| Title |
FCHL-CHD patient 5 [GPL92] |
| Sample type |
RNA |
| |
|
| Source name |
subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 5
|
| Organism |
Homo sapiens |
| Characteristics |
chd status: CHD: patient undergoing coronary artery bypass surgery
fchl status: FCHL
tg rsponse to statins status: non-reduced TG
|
| Treatment protocol |
Tissue was excised from upper abdominal subcutaneous region and immediately snap-frozen in the operating room.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized to Affymetrix Genechips for 16 hr at 45°C and GeneChips were washed and stained in an Affymetrix Fluidics Station according to standard Affymetrix protocols.
|
| Scan protocol |
Performed according to standard Affymetrix protocols.
|
| Description |
Gene expression data from upper abdominal subcutaneous adipose tissue of CHD patient with FCHL
|
| Data processing |
Image-files were analysed with Bioconductor in R using the pmonly and rma algorithms implemented in expresso. Normalisation of chip sets was performed by the ‘quantiles’ approach and probe sets summarised using ‘median polish’. Probes were labelled ‘absent’ or ‘present’ according to the Affymetrix Microarray Suite 5.0 algorithm. Probes returning absent calls in all cel files were removed. Differences in probe values were detected by the Significance Analysis of Microarray (SAM) procedure at specified false detection rates (FDR).
|
| |
|
| Submission date |
Oct 23, 2013 |
| Last update date |
Oct 29, 2013 |
| Contact name |
Carol Shoulders |
| Organization name |
QMUL
|
| Department |
Centre for Endocrinology
|
| Street address |
Charterhouse Square
|
| City |
London |
| ZIP/Postal code |
EC1M 6BQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL92 |
| Series (1) |
| GSE51625 |
Expression data from human abdominal, subcutaneous adipose tissue |
|
