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All rights reserved. http://resource.belframework.org/belframework/20131211/knowledge/large_corpus.bel http://purl.org/dc/elements/1.1/title BEL Framework Large Corpus Document http://resource.belframework.org/belframework/20131211/knowledge/large_corpus.bel http://purl.org/pav/authoredBy http://www.tkuhn.ch/bel2nanopub/RAQFBehjjmEY1ZLnhLUBK65vlXvO0MndOMqYmymK8B5QI#_5 http://resource.belframework.org/belframework/20131211/knowledge/large_corpus.bel http://purl.org/pav/version 20131211 http://www.tkuhn.ch/bel2nanopub/RAQFBehjjmEY1ZLnhLUBK65vlXvO0MndOMqYmymK8B5QI#_4 http://www.w3.org/ns/prov#value Four wild type and three Foxa3?/? testes samples, each containing 1 ?g of total RNA, were hybridized after a single round of amplification to Affymetrix MOE430v2 oligo chips. Data was provided as absent/present calls and intensity values. We normalized the data using the GeneChip Robust Multi-Array Analysis (GCRMA) algorithm (Wu et al., 2003), implemented in a R package (http://www.bioconductor.org/repository/devel/vignette/gcrma.pdf). Fold-changes were calculated as the ratio of the geometric mean between wild type and Foxa3?/? intensities. Statistical analysis of the microarray data was completed using the significance of microarrays (SAM) (Tusher et al., 2001) package with a false discovery rate (FDR) of 10% and fold change cutoff of absolute value of 2.0. Annotation for each ‘spot’ was downloaded from the Affymetrix web site. The data has been deposited into ArrayExpress. Individual steady state transcript levels were determined by real time PCR (QPCR) using the SYBR Green Master Mix from Stratagene on a Stratagene MX3000 QPCR instrument. RNase protection analysis was basically carried out as described previously (Kaestner et al., 1994) using the RPAII kit from Ambion (Austin, TX, USA). The protected RNA fragments were separated on 8 M urea denaturing 6% acrylamide gels and the radioactive bands visualized using a PhosphoImager (Molecular Dynamics). Primer sequences used can be obtained from Kaestner Lab website (http://www.med.upenn.edu/kaestnerlab/reagents.shtml). Overall, the gene expression profiles were similar between wild type and homozygous mutant mice, indicating that there is no global mis-regulation of transcription in Foxa3-deficient testes. However, the mRNA levels of several genes specifically expressed in germ and Leydig cells were significantly affected by the absence of Foxa3 (Table I). 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