Fig. 1

Imprinted gene expression in rat embryonic and extraembryonic cells. a Experimental design. Two distinct reciprocal crosses of rat strains (BN/CrlCrlj, “B” and WKY/NCrlCrlj, “W” and F344/NSlc, “F”) were conducted and cells from the E8.5 epiblast (Epi) and the ectoplacental cone (EPC) were collected. RNAseq was performed on all samples (in duplicate or triplicate), and WGBS was performed in duplicate on BW/WB matings. The maternal (red) strain is listed first in cross names. b Scatterplot of paternal expression ratios in rat EPCs. The paternal expression ratio was averaged over 11 samples, and expressed transcripts (RPKM ≥1) with sufficient allelic coverage (RPM ≥0.5) in at least 6 samples are shown (n=16,642). Transcripts showing parent-of-origin imprinted gene expression (Student’s t test, Bonferroni-adjusted p-val <0.05) are colored red (maternally expressed) or blue (paternally expressed). c Rat genome browser screenshots of the maternally expressed imprinted gene H19 and paternally expressed imprinted gene Igf2. For each cross, duplicates or triplicates were merged and the mean expression level is displayed in reads per million (RPM). A subset of all read alignments (gray) are highlighted if they originated from a maternal (red) or paternal (blue) alleles. The genomic position of known Refseq genes and CpG islands (CGIs) are included. d Ideogram karyotype summary of imprinted gene expression identified using a combination of T-test and Limma in rat Epi and EPC cells. Genes that show imprinted gene expression in human or mouse are indicated with an asterisk and tilde, respectively. LOC103691708, Itga1, and genes showing maternal imprinted expression uniquely in EPC cells and normally expressed in adult rat blood (RPKM ≥1) are not shown due to space limitations (see Additional file 2: Table S1 for a full list of imprinted genes)