Genechip operating software gcos v 1.4

Total RNA samples from the corpus and the cauda epididymal regions of three controls and three Dicer1 cKO mice were used to determine the transcript signature found in these regions. Microarray analyses were performed by the CHUQ Gene Expression Platform (Quebec, Canada). Samples were hybridized to the GeneChip Mouse Gene 2.0 ST (Affymetrix). This array encompasses 35,240 transcript probe-sets, from three transcript data sources (i.e. RefSeq, Ensembl and lncRNA db). As described above, microarrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and Affymetrix GeneChip Command Console software (Affymetrix, Santa Clara, CA), to produce the intensity files. The image data were analyzed with Expression Console Software for quality control (Affymetrix) (S2 Fig) and extracted with the GeneChip Operating Software (GCOS v 1.4; Affymetrix). CEL files were imported and analyzed with Partek Genomics Suite 6.5 software (Partek Incorporated). All gene expression microarray data have been deposited in the Gene Expression Omnibus (GEO) repository database for public access (#GSE77139).

Hybridization, fluidics and scanning were performed according to standard Affymetrix protocols (http://www.affymetrix.com) for the GeneChip® Plasmodium/Anopheles Genome Array. GeneChip Operating Software (GCOS v1.4, http://www.Affymetrix.com) was used to convert the image files to cell intensity data. The cell files were input into Partek Genomics Suite software (Partek, inc. St. Louis, Mo.) and quantile normalized to produce the principal components analysis (PCA) graphs. An ANOVA was performed within Partek to obtain multiple test corrected p-values using the false discovery rate (FDR) method⁹² and was combined with fold change values for each comparison of interest.