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Open Access Research article

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

Nolwenn M Dheilly12*, Christophe Lelong1, Arnaud Huvet2 and Pascal Favrel1

Author Affiliations

1 Université de Caen Basse-Normandie, UMR M100 "Physiologie et Ecophysiologie des Mollusques Marins", IBFA, IFR ICORE 146, Esplanade de la Paix, 14032 Caen Cedex, France

2 Ifremer, UMR M100 "Physiologie et Ecophysiologie des Mollusques Marins", Technopole Brest Iroise, 29290 Plouzané, France

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BMC Genomics 2011, 12:468  doi:10.1186/1471-2164-12-468

Published: 27 September 2011

Additional files

Additional file 1:

List of 34 duplicated contigs and the gene expression values obtained within each tissue. This table provides for each probe the sequence: Probe sequence, Row: Row on array, Col: Column on array, ProbeName, ContigName: Sigenae accession number, GB_ACC: GenBank accession number, Description: Description from Gigas Database, Duplicate probes: GenBank accession number of corresponding duplicated probe, GI: Gills; G: gonad; DG: Digestive gland; M: Mantle; MS: Adductor muscle; P: Labial palps; GG: Visceral ganglia; HE: Hemocytes, R2: Coefficient of determination.

Format: XLS Size: 105KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

List of 200 putative genes constituted of at least 2 different contigs that show extremely similar gene expression profiles. This table provides for each gene the ID genbank: accession number, Description from GigasDatabase, GeneName: gene name as cited in the text, mean: mean log normalized gene expression, stdev: standard deviation of log normalized gene expression, CV: coefficient of variation, max: maximum value, Min: minimum value, MFC: maximum fold change, mean R2: mean Coefficient of determination.

Format: XLSX Size: 80KB Download file

Open Data

Additional file 3:

Housekeeping genes and tissue-enriched contigs selected for quantitative RT-PCR assay. This table provides for each contig the spot: location on microarray, ID genbank: accession number, length of primers (nucleotides), seq: 5' to 3' sequence of primer.

Format: XLS Size: 36KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Comparison of gene expression profiles of tissue-enriched contigs measured by microarray and quantitative RT-PCR analysis. Strong homologies were observed with a coefficient of correlation (R2) ranging from 65 to 93%. Letters identify the tissue (GI: Gills; G: gonad; DG: Digestive gland; M: Mantle; MS: Adductor muscle; P: Labial palps; GG: Visceral ganglia; HE: Hemocytes).

Format: PPT Size: 464KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 5:

Lists of tissue-enriched contigs: male gonad, female gonad, gills, labial palps, digestive gland, mantle, adductor muscle, visceral ganglion, hemocytes. This table provides for each contig the spot: location on microarray, ID genbank: accession number, Description from GigasDatabase, GeneName: gene name as cited in the text, mean: mean log normalized gene expression, stdev: standard deviation of log normalized gene expression, GI: Gills; G: gonad; DG: Digestive gland; M: Mantle; MS: Adductor muscle; P: Labial palps; GG: Visceral ganglia; HE: Hemocytes, SS: sum of squares, df: degrees of freedom, F ratio: ratio of the model mean square to the error mean square, adj p value: adjusted Bonferroni's correction p value.

Format: XLS Size: 911KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Lists of contigs gonad-enriched, gills- and labial palps-enriched, and ganglion- and hemocyte-enriched. This table provides for each contig the spot: location on microarray, ID genbank: accession number, Description from GigasDatabase, GeneName: gene name as cited in the text, mean: mean log normalized gene expression, stdev: standard deviation of log normalized gene expression, GI: Gills; G: gonad; DG: Digestive gland; M: Mantle; MS: Adductior muscle; P: Labial palps; GG: Visceral ganglia; HE: Hemocytes, SS: sum of squares, df: degrees of freedom, F ratio: ratio of the model mean square to the error mean square, adj p value: adjusted Bonferroni's correction p value.

Format: XLS Size: 4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

125 candidate reference genes identified within this study. This table provides for each gene the spot: location on microarray, ID genbank: accession number, Stdev: standard deviation, CV: coefficient of variation, max: maximum value, min: minimum value, MFC: maximum fold change.

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

RNA integrity. Provides the method employed to measure RNA integrity in oyster samples.

Format: DOCX Size: 138KB Download file

Open Data

Additional file 9:

GigasDatabase version 6. All sequences of GigasDatabase version 6 in Fasta format.

Format: ZIP Size: 7.7MB Download file

Open Data