|
| Status |
Public on Jul 25, 2013 |
| Title |
Blood_OJcontrol_T4_S54 |
| Sample type |
RNA |
| |
|
| Source name |
whole blood, OJ time 4
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
tissue: whole blood
intervention: OJ time 4
|
| Treatment protocol |
Blood was pulled directly into Paxgene tubes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the protocol provided with the Paxgene tubeswith the optional on-column DNase treatment
|
| Label |
biotin
|
| Label protocol |
For the OJcontrol samples 50 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplification System V2 (Nugen Technologies). Microarray template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.). For the alcohol experimental samples 50 ng total RNA was reverse transcribed and amplified using the 3' IVT one-cycle kit (Affymetrix), fragmented and biotin labeled using the GeneChip IVT labeling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
|
| Scan protocol |
Scanning done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
|
| Description |
08CHT054T4.CEL
|
| Data processing |
GCOS report derived with TGT Value set at 500. The ethanol data was imported as CEL files into S+ArrayAnalyzer™ (version 2.1.1). Tools available in ArrayAnalyzer were used to assess data quality at the chip level. Background subtraction and summarization was done with RMA [Irizarry, 2003] and GCRMA, and the summarized data was quantile normalized [Bolstad, 2003]. RMA summarized data was filtered for log2 (RMA expression) >6 in at least six chips; GCRMA summarized data was filtered for log2 (GCRMA expression) >5. Each list was further filtered for a fold change in at least one pairwise comparison greater than 1.25. The Local Pooled Error (LPE T-test) [Jain, 2003] was used for differential expression testing across all possible pairwise timepoint comparisons. The False Discovery Rate (FDR) was controlled by implementation of the Benjamini and Hochberg correction [Benjamini, 1995]. Statistically significant genes (p<0.05) from the ten pairwise timepoint comparisons from both the RMA and GCRMA summarized data were combined into one list. A second list of significant genes was generated using the application, EDGE (Storey, 2007). RMA summarized data filtered for expression as above was used for input. The resulting list, ranked by Q-value, was filtered for a fold change in at least one pairwise comparison greater than 1.25.
|
| |
|
| Submission date |
Feb 23, 2010 |
| Last update date |
Apr 29, 2015 |
| Contact name |
Dennis M Burian |
| E-mail(s) |
dennis.burian@faa.gov
|
| Phone |
405-954-6087
|
| Organization name |
Federal Aviation Administration
|
| Department |
Aviation Medicine
|
| Lab |
Bioaeronautical Sciences Research Lab
|
| Street address |
6500 S. MacArthur Blvd., AAM610
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73169 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE20489 |
Microarray characterization of gene expression changes in blood during acute ethanol exposure |
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