Transcriptome changes after genome wide admixture in invasive sculpins

European sculpins (Cottus) harbor an example of a recent hybrid speciation event, which entails the invasion of a new habitat by the hybrid species. We compare the transcriptomes of both parental species and the hybrid species to understand how they differ. F2 crosses between the parent species are compared to the hybrid species and its parent species to identify unique patterns of the hybrid species due to the initial hybridization process or respectively to other processes. See the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology no doi yet) for more information. The transcriptome was compared between an invasive hybrid species of Cottus (Sieg population n = 8) and its parent species C.rhenanus and C.perifretum. Expression profiles of both parental populations were assessed by two independent replicate population (C.rhenanus: Broel and Naaf; C.perifretum Laarse Beek and Witte Nete; each population n = 8). The transcriptomes of F2 crosses between the populations of C.rhenanus and C.perifretum were assessed with for independent crosses with 4 biological replicates for each cross (n = 4 x 4 = 16). We used a custom design microarray with probes designed based on transcriptome sequencing. We used a newly developed calibration method to account for differences in individual probe binding behavior and to detect and remove probes unfit for analysis. Data stored as “normalized data” are normalized and quality filtered based on this new calibration method and normalized for interarray comparability by division by the 75%tile signal intensity for each array. Please refer to the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology; no doi yet) for more information.