Open Access Research article

Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts

Josep A Calduch-Giner1, Azucena Bermejo-Nogales1, Laura Benedito-Palos1, Itziar Estensoro2, Gabriel Ballester-Lozano1, Ariadna Sitjà-Bobadilla2 and Jaume Pérez-Sánchez1*

Author Affiliations

1 Nutrigenomics and Fish Growth Endocrinology Group, Department of Marine Species Biology, Culture and Pathology, Institute of Aquaculture Torre de la Sal, Castellón, CSIC, Spain

2 Fish Pathology Group, Department of Marine Species Biology, Culture and Pathology. Institute of Aquaculture Torre de la Sal, Castellón, CSIC, Spain

For all author emails, please log on.

BMC Genomics 2013, 14:178  doi:10.1186/1471-2164-14-178

Published: 15 March 2013

Additional files

Additional file 1:

Complete list of IPA canonical pathways, with the ratio of gilthead sea bream sequences of the reported transcriptome detected for each one.

Format: PDF Size: 295KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Biological networks of genes linked to the canonical pathways “mTOR Signaling” (A), “Mitochondrial Dysfunction” (B), “Tight Junction Signaling” (C), “B Cell Receptor Signaling” (D), “Acute phase response signaling” (E) and “Complement System” (F) according to Ingenuity Pathway Analysis. Genes that are present in the gilthead sea bream nucleotide database are shown with grey shading. Direct interactions are shown as solid lines and indirect as dashed lines.

Format: PDF Size: 887KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Post-processing data and pipeline for frameshift correction. Zip file contains a Word document with an explanation of the distinct steps of the frameshifts processing pipeline accompanied by a graphical description of the pipeline schematics, and an Excel document reporting the frameshift corrections.

Format: ZIP Size: 2.4MB Download file

Open Data