Computational protocol: Mouse BRWD1 is critical for spermatid postmeiotic transcription and female meiotic chromosome stability

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Protocol publication

[…] RNA extracted from WT and mutant testes was analyzed for quality using BioAnalyzer (Affymetrix). They were then converted to biotin-labeled complementary RNA (cRNA) fragments according to the protocols described by Affymetrix. Hybridization was performed using Affymetrix MOE430 2.0 gene chips that represent >39,000 uniquely expressed mouse transcripts. Washing and scanning were also done according to Affymetrix protocols. The signals from scanning were analyzed using GCOS software (Affymetrix). The normalized signals were then analyzed using R software using a standard t test, and genes were considered up- or down-regulated if they showed a more than twofold difference in expression with a p-value of <0.01. Genes were classified as meiotic, postmeiotic, or somatic using the BioMart mining tool available at the GermOnline database (http://www.germonline.org/index.html). Gene ontology (GO) analysis of the misexpressed genes was performed using DAVID (). We used the MGI database (http://www.informatics.jax.org/) to search for any known knockout phenotypes of genes misregulated in the microarray. […]

Pipeline specifications

Software tools BioMart, DAVID
Databases GermOnline
Application Genome annotation
Organisms Mus musculus
Diseases Deficiency Diseases