Crassostrea gigas male gonad transcriptomic 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.v4; https://figshare.com/articles/dataset/Crassostrea_gigas_male_gonad_transcriptional_data_comparison/1004464/4

This fileset represents a comparison of RNA-seq data from a Pacific oyster (Crassostrea gigas) male gamete library to microarray data from Dheilly et al. 2012. Specifically sequence reads were mapped to full-length transcripts represented on the array platformed used by Dheilly et al 2012. "Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes". Data was joined using SQLShare. File Descriptions: Fastafile - fasta file corresponding to targets on microarray. Used for RNA-seq analysis. Rcode_OlsonandRoberts.R - The R code used to visualize expression levels of RNA-Seq data relative to clusters of gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. 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 - Tab-delimited file that includes Dheilly et al table S1 and corresponding RNA-seq data from single male gamete library. Dheilly_DiffGametogenesis_S2_GonadRNAseq.txt - Tab-delimited file that includes Dheilly et al table S2 and corresponding RNA-seq data from single male gamete library. 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