File S1 - Alterations of Epigenetic Signatures in Hepatocyte Nuclear Factor 4α Deficient Mouse Liver Determined by Improved ChIP-qPCR and (h)MeDIP-qPCR Assays

Figure S1, Effects of Hnf4a deficiency on histone H3 lysine 4 dimethyl (H3K4me2) and histone H3 lysine 4 trimethyl (H3K4me3) in female mouse livers. Enrichment of H3K4me2 and H3K4me3 at specific loci relative to input in ChIPed DNA fragments in livers from female Hnf4a-LivKO and wild-type mice was normalized by the positive control. Insets, the percentage of total ChIPed DNA fragments relative to input for H3K4me2 and H3K4me3 in livers from female Hnf4a-LivKO and wild-type mice. Negative = negative control. Mean ± S.E., N = 3 biological replicates. *, pHnf4a-LivKO and wild-type mice was normalized by the positive control. Insets, the percentage of total ChIPed DNA fragments relative to input for H3K9me2 and H3K9me3 in livers from female Hnf4a-LivKO and wild-type mice. Negative = negative control. Mean ± S.E., N = 3 biological replicates. *, pHnf4a-LivKO and wild-type mice was normalized by the positive control. Insets, the percentage of total ChIPed DNA fragments relative to input for H3K27me3 and H3K4ac in livers from female Hnf4a-LivKO and wild-type mice. Negative = negative control. Mean ± S.E., N = 3 biological replicates. *, pHnf4a deficiency. Table S3, List of qPCR primers used for IPed DNA fragments and cDNA. (PDF)