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Sample GSM514739 Query DataSets for GSM514739
Status Public on Jul 25, 2013
Title Blood_alcohol_T3_S13
Sample type RNA
 
Source name whole blood, BAC 0.08%
Organism Homo sapiens
Characteristics gender: male
tissue: whole blood
intervention: BAC 0.08%
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 CHT_S13_T3_12.09.04.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

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
1007_s_at 6.50260267418102
1053_at 5.95425616529647
117_at 8.23964967485686
121_at 8.03621226547698
1255_g_at 3.90444118173796
1294_at 7.3909832267024
1316_at 6.73342401390311
1320_at 5.99525059492328
1405_i_at 10.6985705973881
1431_at 3.51994771164796
1438_at 5.90877732630088
1487_at 7.25540468004544
1494_f_at 5.67094162398237
1552256_a_at 6.34817909955505
1552257_a_at 6.62449241524784
1552258_at 5.918158984764
1552261_at 5.82779069751522
1552263_at 7.97258083272104
1552264_a_at 8.47772074745136
1552266_at 3.77423685046212

Total number of rows: 54675

Table truncated, full table size 1478 Kbytes.




Supplementary file Size Download File type/resource
GSM514739.CEL.gz 8.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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