Open Access Highly Accessed Research article

Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

Yuliaxis Ramayo-Caldas1*, Nuria Mach234, Anna Esteve-Codina1, Jordi Corominas1, Anna Castelló1, Maria Ballester1, Jordi Estellé234, Noelia Ibáñez-Escriche5, Ana I Fernández6, Miguel Pérez-Enciso178 and Josep M Folch18

Author Affiliations

1 Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain

2 INRA, UMR 1313 Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique Immunité Santé, Jouy-en-Josas, F-78352, France

3 AgroParisTech, UMR 1313 GABI, Jouy-en-Josas, F-78352, France

4 CEA, DSV/iRCM/SREIT/LREG, Jouy-en-Josas, F-78352, France

5 Genètica i Millora Animal, IRTA Lleida, Lleida, 25198, Spain

6 Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain

7 Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

8 Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain

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BMC Genomics 2012, 13:547  doi:10.1186/1471-2164-13-547

Published: 11 October 2012

Additional files

Additional file 1:

Table S1. Phenotypic means comparison ± standard deviation between the sequenced individuals.

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Additional file 2:

Figure S1. Profile of gene expression distribution in both High and Low groups.

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Additional file 3:

Figure S2. Correlations between expression values of genes analysed by both RNA-seq and Affymetrix microarray technologies. X-axis values are the log2 of expression quantified with Affymetrix Microarray technology and y-axis are values of log2 (FPKM).

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Additional file 4:

Table S2. Description of the repetitive elements identified in the pig liver transcriptome.

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Additional file 5:

Figure S3. Venn diagrams of the predicted lncRNA.

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Additional file 6:

Figure S4. Per-gene estimates of the base variance against the base levels. The red line represents the fit variance. X-axis values are the base mean and y-axis values are the log10 of the base mean and y-axis values are the log10 of the base variance.

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Additional file 7:

Figure S5. Curves of the empirical cumulative density functions in both H and L groups. X-axis values are the chi-squared probability of residual and y-axis values are the empirical cumulative density functions.

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Additional file 8:

Figure S6. Estimated variances as squared coefficients of variation produced with the function ‘scvPlot’. X-axis values are the base mean and y-axis values are the squared coefficients of variation.

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Additional file 9:

Table S3. Comparison between RNA-seq (Htseq) and RT-qPCR (relative quantification) expression data of APOA2, LPIN1, ME3, CYP7A1 and CYP2C49 genes. Relative CNV data for CYP2C49 in comparison to the reference individual H3 is indicated in the last column.

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Additional file 10:

Figure S7. Network 2 as generated by IPA. The significant biological functions comprising this network are Lipid Metabolism, Molecular Transport and Small Molecule Biochemistry. The network is displayed graphically as nodes (gene/gene products) and edges (the biological relationship between nodes). The node colour indicates the expression of genes: red up-regulated, green down-regulated in H group relative to L group. The shapes of nodes indicate the functional class of the gene product.

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Additional file 11:

Figure S8. Network 3 as generated by IPA. The significant biological functions comprising this network are Carbohydrate Metabolism, Lipid Metabolism and Molecular Transport. The network is displayed graphically as nodes (gene/gene products) and edges (the biological relationship between nodes). The node colour indicates the expression of genes: red up-regulated, green down-regulated in H group relative to L group. The shapes of nodes indicate the functional class of the gene product.

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Additional file 12:

Table S4. Primers designed for the validation of differentially-expressed genes by RT-qPCR and copy number determination by qPCR.

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