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Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors

Cecilia C Sánchez123, Gregory M Weber2, Guangtu Gao2, Beth M Cleveland2, Jianbo Yao3 and Caird E Rexroad2*

Author Affiliations

1 Shepherd University, Institute of Environmental and Physical Sciences, Robert C. Byrd Science and Technology Center, Shepherdstown, WV, 25443, USA

2 USDA/ARS/NCCCWA, 11861 Leetown, Kearneysville, WV, 25430, USA

3 West Virginia University, Animal and Nutritional Sciences, Morgantown, WV, 26506, USA

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BMC Genomics 2011, 12:626  doi:10.1186/1471-2164-12-626

Published: 21 December 2011

Additional files

Additional File 1:

Table S1 Water Quality Parameters, Table S2 Gene Ontology Annotation. Table S1 contains temperature, dissolved oxygen, carbon dioxide, pH, ammonia, and nitrite data for each of the time periods and treatments. Table S2 contains transcriptome annotation assignments including BLASTx hits and Gene Ontology terms. Additional file 1: Additional File 1 Water Quality and GO.xlsx, 11694K webcite

Format: XLSX Size: 11.4MB Download file

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Additional File 2:

Gene Ontology Figures, Figures S1 and S2 in a PDF. Figures show the distribution of Gene Ontology hits by GO level as broken down by Biological Brocess (P), Molecular Function (F) and Cellular Component (C) (Figure S1). A second figure shows assignment of Gene Ontology categories broken down by Biological Processes (a), Molecular Functions (b) and Cellular Components (c) (Figure S2). Additional file 2: Additional File 2 Gene Ontology Results.pdf, 934K webcite

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Additional File 3:

Table S3 Newbler SNP Discovery, Table S4 MIRA3 SNP Discovery. Table S3 contains information for 57,207 putative SNPs identified from Newbler reference transcriptome contigs. Table S4 contains information for 808 putative SNPs identified from MIRA3 reference transcriptome contigs. Additional File 3: Additional File 3 SNPs.xlsx, 11083K webcite

Format: XLSX Size: 10.8MB Download file

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