Data from: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.Normalized small RNA read counts from whole seedsNormalized reads per million (RPM) values in 300 bp windows across the entire A. thaliana genome for 21-24 nucleotide small RNAs from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, CvixCol and ColxCvi whole seeds 6 days after pollination.norm.s.txt.sRNAfiles.tar.gzAllele-specific classification of small RNAs from whole seedsSmall RNAs overlapping Col-Cvi or Col-Ler SNPs were classified according to strain origin from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, ColxCvi and CvixCol whole seeds 6 days after pollination.SNP_counts.txt.sRNAfiles.tar.gzMean methylation in Arabidopsis embryo and endospermMean methylation in overlapping 300 bp windows for embryo and endosperm from ColxCol, LerxLer, CvixCvi, CvixCol, ColxCvi, LerxCvi, and CvixLer seeds dissected 6 days after pollination. CG, CHG, and CHH methylation are quantified in separate files.window.mean.tar.gzWeighted methylation in Arabidopsis embryo and endospermWeighted methylation values in 300 nt windows for Arabidopsis embryo and endosperm from ColxCol, LerxLer, CvixCvi, ColxCvi, CvixCol, LerxCvi, and CvixLer seeds dissected 6 days after pollination.weighted_summary.tar.gzmRNA-seq read counts for Arabidopsis embryo and endospermTotal and allele-specific mRNA-seq read counts, along with FPKM values, are quantified for genes and TEs from embryo and endosperm tissue from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, ColxCvi, CvixCol, LerxCvi and CvixLer seeds dissected 6 days after pollination, along with whole seeds from ColxCvi and CvixCol.stats_per_locus.tar.gzAllele-specific mRNA SNP counts for Arabidopsis embryo and endospermThe number of mRNA-seq reads matching each Col-Ler, Col-Cvi, or Ler-Cvi SNP is reported for data from ColxLer, LerxCol, ColxCvi, CvixCol, LerxCvi, and CvixLer embryo and endosperm dissected 6 days after pollination, along with ColxCvi and CvixCol whole seeds.snp_counts.tar.g