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". Sp...
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ftdatacite:10.6084/m9.figshare.1004464.v6 2023-05-15T15:57:37+02:00 Crassostrea gigas male gonad transcriptome data comparison Olson, Claire Roberts, Steven 2014 https://dx.doi.org/10.6084/m9.figshare.1004464.v6 https://figshare.com/articles/dataset/Crassostrea_gigas_male_gonad_transcriptional_data_comparison/1004464/6 unknown figshare https://dx.doi.org/10.6084/m9.figshare.1004464 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Physiology FOS Biological sciences Marine Biology 60102 Bioinformatics FOS Computer and information sciences Genetics Molecular Biology dataset Dataset 2014 ftdatacite https://doi.org/10.6084/m9.figshare.1004464.v6 https://doi.org/10.6084/m9.figshare.1004464 2021-11-05T12:55:41Z 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 Dataset Crassostrea gigas Pacific oyster DataCite Metadata Store (German National Library of Science and Technology) Dubos ENVELOPE(-57.250,-57.250,-63.883,-63.883) Pacific |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
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ftdatacite |
language |
unknown |
topic |
Physiology FOS Biological sciences Marine Biology 60102 Bioinformatics FOS Computer and information sciences Genetics Molecular Biology |
spellingShingle |
Physiology FOS Biological sciences Marine Biology 60102 Bioinformatics FOS Computer and information sciences Genetics Molecular Biology Olson, Claire Roberts, Steven Crassostrea gigas male gonad transcriptome data comparison |
topic_facet |
Physiology FOS Biological sciences Marine Biology 60102 Bioinformatics FOS Computer and information sciences Genetics Molecular Biology |
description |
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 |
format |
Dataset |
author |
Olson, Claire Roberts, Steven |
author_facet |
Olson, Claire Roberts, Steven |
author_sort |
Olson, Claire |
title |
Crassostrea gigas male gonad transcriptome data comparison |
title_short |
Crassostrea gigas male gonad transcriptome data comparison |
title_full |
Crassostrea gigas male gonad transcriptome data comparison |
title_fullStr |
Crassostrea gigas male gonad transcriptome data comparison |
title_full_unstemmed |
Crassostrea gigas male gonad transcriptome data comparison |
title_sort |
crassostrea gigas male gonad transcriptome data comparison |
publisher |
figshare |
publishDate |
2014 |
url |
https://dx.doi.org/10.6084/m9.figshare.1004464.v6 https://figshare.com/articles/dataset/Crassostrea_gigas_male_gonad_transcriptional_data_comparison/1004464/6 |
long_lat |
ENVELOPE(-57.250,-57.250,-63.883,-63.883) |
geographic |
Dubos Pacific |
geographic_facet |
Dubos Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
https://dx.doi.org/10.6084/m9.figshare.1004464 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.1004464.v6 https://doi.org/10.6084/m9.figshare.1004464 |
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1766393297011474432 |