This article is part of a special issue on epigenomics.

Open Access Research

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

Michael K Skinner1*, Mohan Manikkam1, Md M Haque1, Bin Zhang2 and Marina I Savenkova1

Author Affiliations

1 Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA

2 Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY 10029, USA

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Genome Biology 2012, 13:R91  doi:10.1186/gb-2012-13-10-r91

Published: 3 October 2012

Additional files

Additional file 1:

Figure S1 - microarray histogram quality control. (a-l) Sample histograms and box plots for microarray raw (a) and pre-processed signal values, using a RMA (Robust Multiarray Average), GC-content-adjusted algorithm for 11 male and female tissues (b-l).

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Additional file 2:

Figure S2 - cluster coefficient and connections. (a,b) Cluster coefficient versus number of connections for male (a) and female (b) network modules.

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Additional file 3:

Figure S3 - gene networks from gene modules. (a-d) Direct connection sub-networks for female and male modules: (a) female turquoise; (b) male yellow; (c) male brown; (d) male turquoise. Shape and color codes are the same as for Figure 5.

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Additional file 4:

Figure S4 - gene networks from signature lists. (a-d) Direct connection sub-networks for female and male tissue signature lists: (a) female heart; (b) female kidney; (c) male ovary; (d) uterus; (e) male heart; (f) male kidney; (g) male liver. Shape and color codes are the same as for Figure 5.

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Additional file 5:

Table S1 - differentially expressed genes in tissues.

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Additional file 6:

Table S2 - pathway enrichment in signature lists.

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Additional file 7:

Table S3 - pathway enrichment in tissue modules.

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Additional file 8:

Table S4 - epigenetic control regions and gene expression.

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Additional file 9:

Table S5 - lncRNA and epigenetic control regions.

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