|
| Status |
Public on Aug 22, 2013 |
| Title |
HVc, biological rep5 (LD) |
| Sample type |
RNA |
| |
|
| Source name |
HVC
|
| Organism |
Serinus canaria |
| Characteristics |
age: adult
tissue: HVC
light cycle: long day
|
| Treatment protocol |
none
|
| Growth protocol |
Adult canaries housed in long light cycles in aviaries
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with micro-scalpels (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into Qiazol (Qiagen) and stored at -80C till RNA preparation.
|
| Label |
biotin
|
| Label protocol |
RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.
|
| |
|
| Hybridization protocol |
The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.
|
| Scan protocol |
The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.
|
| Description |
Can_LD_male_HVC_22
HVC was dissected from cryosections
|
| Data processing |
The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: E26R1204 Genomatix GmbH (http://www.genomatix.de)
ChipInspector fold changes directly generated from the CEL files (i.e. no normalized data for each sample), performing significance analysis on the single probe level.
The *Ento.txt files (on Series records) contains the differential expression data analyzed using the group-wise exhaustive analysis: HVc (or RA) samples group compare to Ento samples group with False Discovery Rate set to zero and 10-significant probe minimum coverage. These result files consist in the table of transcripts and the fold changes for every data combination, also chromosome location (in TGU), Gene ID, Gene Symbol. The statistic algorithm in ChipInspector is a T-test with a permuted artificial background. It is based on and enhances the original SAM algorithm by Tusher et al. (2001): Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98(9), pp 5116-5121. Exhaustive matching of the experiments introduces a second level of data volume enhancing. This means it is using the complete set of available data points by matching the values from every condition experiment to the values from every control experiment. This gives the results greater confidence and therefore increases the number of values that are recognized as significant (higher number of significant genes with lower FDR) (http://www.genomatix.de).
|
| |
|
| Submission date |
Aug 21, 2013 |
| Last update date |
Jan 31, 2014 |
| Contact name |
Carolina Frankl-Vilches |
| E-mail(s) |
frankl@orn.mpg.de
|
| Phone |
00498157932402
|
| Organization name |
Max Planck Institute for Ornithology
|
| Department |
Behavioural Neurobiology
|
| Street address |
Eberhard-Gwinner-Str. 6a
|
| City |
Seewiesen-Starnberg |
| State/province |
Bavaria |
| ZIP/Postal code |
82319 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17605 |
| Series (1) |
| GSE50070 |
Expression data from Serinus canaria HVC, RA and Entopallium |
|
