|
| Status |
Public on Feb 26, 2013 |
| Title |
male brain 111, control |
| Sample type |
RNA |
| |
|
| Source name |
Zebrafish male adult brain control
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole brain
strain: Transgenic Mosaic 1
age: 1 year old (sexually mature adult)
Sex: male
treatment: control
|
| Treatment protocol |
1 year old sexually mature adult zebrafish were fed diets with either control levels of selenium (1.4ppmSe) or supplemented with sodium selenite (5.6ppmSe) for 14 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from whole brains was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
For each array, 10 μg 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, Santa Clara, CA, USA).
|
| |
|
| Hybridization protocol |
Affymetrix Zebrafish Genome Arrays (~14,900 transcripts) were hybridized with fragmented biotinylated cRNA for 16 h at 45 °C with constant rotation (45 rpm), 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.
|
| Scan protocol |
Another round of SAPE was performed prior to scanning using a GeneChip Scanner 3000 (Affymetrix). All microarray procedures were performed at the Genomics Core Facility of the Center for Reproductive Biology at Washington State University (Pullman, WA).
|
| Data processing |
CEL files containing raw data were processed and analyzed using R software and Bioconductor packages. Microarray data were examined for physical anomalies on the chip by pseudo chip and residual error visualizations. Quality Assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport. The arrays were pre-processed using the Robust Multi-array Average (RMA) procedure using the affy package. Next, unexpressed and low variability genes were removed by unbiased filtering. Probesets with less than a median log2 signal value of 5.00 were removed from further analysis. A filter on interquartile range was also applied to remove low variability genes. Genes with an interquartile range of less than 0.5 across all chips in the experiment were excluded. We performed an additional filtration step to reduce the genes down to annotated Ensembl genes.
|
| |
|
| Submission date |
Feb 25, 2013 |
| Last update date |
Feb 26, 2013 |
| Contact name |
Maia J Benner |
| E-mail(s) |
maiabenner@gmail.com
|
| Organization name |
University of Idaho
|
| Department |
Biological Sciences
|
| Lab |
Barrie Robison
|
| Street address |
875 Perimeter Drive
|
| City |
Moscow |
| State/province |
Idaho |
| ZIP/Postal code |
83844-3051 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE44623 |
Transcriptional responses of the zebrafish (Danio rerio) brain to acute sodium selenite supplementation. |
|
