Data · dataset · 2014
Crassostrea gigas male gonad transcriptome data comparison
Listed in DataCite
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".
Description
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.
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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
Links
Where it is published
- Repository landing page figshare.com/articles/dataset/Crassostrea_gigas_male_gonad_transcriptional_… ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.1004464 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.1004464 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.1004464 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Biological sciences · Computer and information sciences
- Inferred from text
- RNA sequencing 65% · Tabular 65%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.1004464 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:biological-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:computer-and-information-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:tabular | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (65%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |