Crassostrea gigas male gonad transcriptional data comparison

• Main Authors: Olson, Claire, Roberts, Steven
• Format: Dataset
• Language: unknown
• Published: figshare 2014
• Subjects: Physiology; FOS Biological sciences; Marine Biology; 60102 Bioinformatics; FOS Computer and information sciences; Genetics; Molecular Biology; Dubos; Ewing; Fang; McCue; Pacific; Crassostrea gigas; Pacific oyster
• Online Access: https://dx.doi.org/10.6084/m9.figshare.1004464.v2; https://figshare.com/articles/dataset/Crassostrea_gigas_male_gonad_transcriptional_data_comparison/1004464/2

This fileset contains transcriptomic data results for the Pacific oyster ( Crassostrea gigas) male gonad tissue in relation with that previously described by Dheilly et al. 2012. File Descriptions: SupplFig_OlsonandRoberts.pdf - Boxplots of expression levels (RPKM) from RNA-Seq data relative to the 10 clusters of similar gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. The number of genes represented are 511 (Cluster 1), 222 (Cluster 2), 312 (Cluster 3), 197 (Cluster 4), 226 (Cluster 5), 146 (Cluster 6), 200 (Cluster 7), 295 (Cluster 8), 332 (Cluster 9), and 41 (Cluster 10). Dheilly_SexSpecific_S1_GonadRNAseq.txt - The expression values we obtained for sex specific genes are represented in this file. Dheilly_DiffGametogenesis_S2_GonadRNAseq.txt - The expression values we obtained within each of the 10 clusters of distinct expression patterns are represented in this file. Overall expression levels were higher in clusters 5 and 6 (average RPKM 156.1 and 174.5, standard deviation 211.8 and 944.9), corresponding to genes exhibiting a change in expression patterns as the oyster gonad is maturing from stage 2 to stage 3 of development during spermatogenesis. Furthermore, clusters 1-4 exhibited very low expression levels, as these clusters correspond to genes differentially expressed during female oogenesis. We observed high expression among genes from cluster 5, corresponding to genes distinct among mature stage 3 spermatozoids/gametes. and therefore conclude that our sample was indeed a mature stage 3 male gonad. References: Dheilly, N. M., Lelong, C., Huvet, A., Kellner, K., Dubos, M., Riviere, G., Boudry, P., and Favrel, Pascal. (2012). Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes. PLoS ONE. 7:e36353-e36353. doi: 10.1371/journal.pone.0036353 Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment. Genome Research. 8: 175-185. doi: 10.1101/gr.8.3.175 Ewing, Brent; Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Research. 8:186-194. doi: 10.1101/gr.8.3.175 Fang, X., Li, L., Luo, R., Xu, F., Wang, X., Zhu, Y., Yang, L., Huang, Z. (2012). Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. doi: http://dx.doi.org/10.5524/100030 Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5:621-628. doi: 10.1038/nmeth.1226