The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of mean background, LOWESS normalization was performed. To assess differential expression of genes, the normalized log intensity ratios (expression ratio) were analyzed with Student's t-test (P <0.05).
Scanning was performed with ScanArray 5000 (GSI Lumonics) and images were processed with GenePix Pro 5.0 (Axon). The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of median background from median signal intensities, the expression ratios (ER) were calculated. Locally weighted non-linear regression (Lowess) normalization was performed, first for the whole slide and next for twelve rows and four columns per slide. The differential expression was assessed by the difference of the mean log2 expression ratios between the slides with reverse labelling (6 spot replicates per gene on each slide, Student´s t-test, p < 0.01). The log2 ER ranked up or down-regulated genes were analyzed interrogating the functional classes of Gene Ontology (GO) and compared by the sums of ranked genes (Student's t-test, p < 0.05).
The slides were pretreated with 1% BSA(fraction V), 20 × SSC, 10% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight in cocktail containing 50 × Denhardt's, 20 × SSC, 10% SDS, 10μg/μl polyadenylate and 10 μg/μl yeast tRNA. All chemicals were from Sigma-Aldrich.
Total RNA from pooled control and TNFα-treated brown trout preovulatory follicles (n = 20) from each of a total of three females was labelled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain) using SuperScript III Transcriptase. The cDNA synthesis reaction was performed at 50ºC for 2 h in a 20 µl reaction volume, followed with RNA degradation with 0.2 M NaOH at 37ºC for 15 min and alkaline neutralization with 0.6 M Hepes. Labeled cDNA was purified with Microcon YM30 (Millipore, Madrid, Spain).
Reproductively mature female brown trout (Salmo trutta) from a cultured stock at the Piscifactoria de Bagà (Generalitat de Catalunya, Bagà, Spain) were kept under natural conditions of temperature and photoperiod. After dissection, brown trout preovulatory ovaries were placed in Hank´s balanced salt solution (HBSS) and individual ovarian follicles were manually separated with forceps from each ovary on ice. To collect ovarian tissue for RNA extraction, preovulatory follicles from each of a total of three females were incubated (400 follicles/50 ml) in HBSS-BSA in the absence or presence of rtTNFα (100 ng/ ml, dissolved directly in HBSS-BSA), at 15ºC for 24 h with gentle shaking (100 rpm). At the end of the incubation follicles (previously de-yolked by gentle pressure) were removed, flash frozen in liquid nitrogen and stored at -80ºC until assayed.
Total RNA from ovarian tissue was isolated using TRIzol Reagent (Invitrogen, Barcelona, Spain), following the manufacturer’s instructions and guidelines. Quantification was carried out with Qubit fluorometer (Invitrogen). cDNA synthesis was performed on 5 μg DNase-treated (RQ1 DNase, Promega, Barcelona, Spain) total RNA using SuperScript III Transcriptase (Invitrogen), oligo(dT) primer and random hexamer primers (Promega), according to the manufacturer's protocols. The RNA was stored at -80°C until use.
VALUE = Normalized log ratio (TNF/CONTROL)