|
| Status |
Public on Mar 27, 2012 |
| Title |
LB_13 |
| Sample type |
RNA |
| |
|
| Source name |
whole fish
|
| Organism |
Cottus perifretum |
| Characteristics |
species/hybrid: Cottus perifretum
population: Laarse Beek (LB)
type: parental
rearing environment: lab reared
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole fishes were homogenized with a Qiagen Tissue Ruptur and total RNA was extracted following the Trizol protocol (Invitrogen). Total RNA was quality accessed using an RNA Nano Chip (Agilent) which a was also used for quantification. Quantification was additionally carried out using a NanoDrop-1000 spectrophotometer
|
| Label |
Cy3
|
| Label protocol |
Labeled cRNA was prepared from total RNA using the Agilent Low Input Quick Amp Labeling kit.
|
| |
|
| Hybridization protocol |
The microarray was loaded with labeled cRNA as described in the Agilent protocol for One-Color Microarray-Based Gene Expression Analysis (version 6.5, May 2010).
|
| Scan protocol |
Microarrays were scanned with an Agilent DNA Microarray Scanner type C with the standard settings for 8 x 15 k Agilent expression arrays.
|
| Data processing |
Feature extraction was carried out using the Agilent Feature Extraction software (version 10.7.3.1) and the “gprocessed signal” was taken in the measure for signal intensity. We employed a new normalization procedure, which relates changes in signal intensity to changes in transcript abundance, thereby accounting for observed large differences in probe-binding behavior. This procedure translates measured signal intensities to a percentage of the target transcript’s abundance in a pool previously used for the calibration of the array. Based on this value, new theoretical signal intensity values are calculated based on the same previous calibration. These new theoretical signal intensity values are then normalized for interarray normalization by division by the 75%tile as suggested by Agilent. For a detailed account of the new normalization procedure, please refer to the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology; no doi yet).
|
| |
|
| Submission date |
Mar 23, 2012 |
| Last update date |
Mar 27, 2012 |
| Contact name |
Till Czypionka |
| Organization name |
MPI for Evolutionary Biology
|
| Department |
Evolutionary Genetics
|
| Lab |
Nolte
|
| Street address |
August-Thienemann-Strasse 2
|
| City |
Ploen |
| ZIP/Postal code |
24306 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15375 |
| Series (1) |
| GSE36755 |
Transcriptome changes after genome wide admixture in invasive sculpins |
|
