Open Access Highly Accessed Research article

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens

Daniel Nätt1, Carl-Johan Rubin2, Dominic Wright1, Martin Johnsson1, Johan Beltéky1, Leif Andersson2 and Per Jensen1*

Author Affiliations

1 IFM Biology, Division of Zoology, Avian Behavioural Genomics and Physiology Group, Linköping University, Sweden

2 Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden

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BMC Genomics 2012, 13:59  doi:10.1186/1471-2164-13-59

Published: 4 February 2012

Additional files

Additional file 1:

Phenotypes of parents and offspring. The behavioural scores and weight data for the animals in the experiment.

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Additional file 2:

Nrs of differentially expressed and methylated genes. Total numbers of significantly differentially expressed genes or methylated promoters (P < 0.05, FDR-corrected) in the different comparisons.

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Additional file 3:

Differentially expressed genes. A full list of all genes found to be differentially expressed, comparing breeds, in both generations, including their chromosomal alignment and accession numbers.

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Additional file 4:

Expression and methylation. Gene expression differences plotted against promoter methylation differences between WL and RJF offspring.

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Additional file 5:

Differentially methylated genes. A full list of all genes, where the promotors were found to be differentially methylated, in both generations.

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Additional file 6:

Gene function. Gene ontology and KEGG pathway annotation for the genes which were either differentially expressed or differentially methylated in both generations, comparing between breeds.

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Additional file 7:

Selective sweep representation. Genes which were differentially expressed or methylated between breeds in both generations, and significantly overrepresented in selective sweeps associated with domestication.

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Additional file 8:

Primer structures. The bisulfate converted primers used in HRM.

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