|
| Status |
Public on Jul 09, 2010 |
| Title |
Blood_statin myopathy_pool_XbaI |
| Sample type |
genomic |
| |
|
| Source name |
statin-induced myopathy patients
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared from whole blood collected in EDTA with a Puregene DNA isolation kit (Gentra Systems).
|
| Label |
biotin
|
| Label protocol |
According to manufacturer (Affymetrix).
|
| |
|
| Hybridization protocol |
DNA was digested with HindIII or XbaI, ligated, PCR amplified, fragmented, end-labeled and hybridized to the chip according the the manufacturers instructions.
|
| Scan protocol |
The arrays were then washed using Affymetrix fluidics station 450 and scanned using the GeneChip Scanner 3000 7G Plus.
|
| Description |
data derived from two pools of 19 and 20 statin myopathy patients
|
| Data processing |
SNP intensity signals were obtained using CEL files generated by Affymetrix GTYPE using the DM algorithm. A general linear regression model (Macgregor S, Visscher PM, Montgomery G, Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates. Nucleic Acids Res 2006; 34(7):e55) was used to identify differences between pools and calculate a z-score (the p-value of the z-test) for each SNP-pool comparison. The data table linked to GSE17574 contains the calculated z-score for each SNP comparing case pools to control pools.
|
| |
|
| Submission date |
Aug 10, 2009 |
| Last update date |
Aug 10, 2009 |
| Contact name |
Paul J. Isackson |
| E-mail(s) |
[email protected]
|
| Organization name |
University at Buffalo
|
| Department |
Pediatrics
|
| Street address |
100 High St
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL2005 |
| Series (1) |
|
