Crassostrea gigas male gonad transcriptome data comparison

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 "Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes". Specifically sequence reads were mapped to full-length transcripts represented on the array platformed used by Dheilly et al 2012. Data was joined using SQLShare.

 

File Descriptions:

Fastafile_Microarray - 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