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Sample GSM220173 Query DataSets for GSM220173
Status Public on Mar 31, 2008
Title Liver 0% carb Male fish11
Sample type RNA
Source name Liver Male 0%carb
Organism Danio rerio
Characteristics adult livers
Seacrest Farms strain
Extracted molecule total RNA
Extraction protocol Extraction using TRIZOL following manufacturer's protocol
Label biotin
Label protocol For each array, up to 10 mg of total RNA were converted to cDNA. Biotinylated cRNA was then produced in vitro using the GeneChip expression 3′ amplification one-cycle target labeling kit (Affymetrix)
Hybridization protocol Microarrays were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 r.p.m.), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody. This was followed by another round of SAPE prior to scanning using a GeneChip Scanner 3000 (Affymetrix).
Scan protocol Scanning was performed using a GeneChip Scanner 3000 (Affymetrix)
Description none
Data processing After hybridization and quality control, probesets were filtered based on the following criteria: First, probesets were eliminated that were not classified as present in all arrays of any one combination of sex and treatment using PMA calls. Second, four separate normalizations of the data (MAS 5, RMA, GCRMA, and PLIER) were performed, and only those probesets that were above the 95th percentile of the background for all four normalizations were retained. The distribution of background intensity values in each case was determined using the negative control probes on the microarray. Ultimately, 6,165 probesets passed the filter criteria and were used in subsequent analyses. Arrays were then clustered based on expression levels of all expressed genes in our filtered set to test for the presence of outlier arrays. In this case, one sample (a male from the 25% carbohydrate treatment) did not cluster with the other arrays and was removed out of concern that this sample harbored contamination from other tissues.
Submission date Aug 23, 2007
Last update date Aug 14, 2011
Contact name Matt L Settles
Phone 5097545396
Organization name University of California, Davis
Department Genome Center
Lab Bioinformatics Core
Street address 451 Health Sciences Sr
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platform ID GPL1319
Series (1)
GSE8856 Sexual dimorphism in the zebrafish hepatic transcriptome and response to dietary carbohydrate

Data table header descriptions
VALUE RMA normalized values

Data table
AFFX-BioB-3_at 5.237223443
AFFX-BioB-5_at 6.553645082
AFFX-BioB-M_at 6.559668024
AFFX-BioC-3_at 7.930620226
AFFX-BioC-5_at 7.535561397
AFFX-BioDn-3_at 10.06259428
AFFX-BioDn-5_at 8.930657213
AFFX-CreX-3_at 12.08596149
AFFX-CreX-5_at 10.978815
AFFX-DapX-3_at 2.575024938
AFFX-DapX-5_at 2.247852662
AFFX-DapX-M_at 2.656925118
AFFX-Dr-AB076373-1_at 2.881205394
AFFX-Dr-acta1-3_at 5.25823505
AFFX-Dr-acta1-5_at 5.65799955
AFFX-Dr-acta1-5_x_at 5.862352859
AFFX-Dr-acta1-M_at 4.130953173
AFFX-Dr-AF292559-1_at 2.510509986
AFFX-Dr-AF292559-2_s_at 2.034074814
AFFX-Dr-AF292559-3_s_at 2.227427884

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.

Supplementary file Size Download File type/resource
GSM220173.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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