Extended Data Figure 2: Validation of H3K4me3 STAR ChIP–seq and RNA-seq in mouse gametes and early embryos.
From: Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
a, Representative bright-field microscopic images showing the pre-implantation embryos used for STAR ChIP–seq with time points of sample collection indicated. b, The Spearman correlation between the replicates (n = 2) of RNA-seq samples and between RNA-seq in this study and Deng et al.36 at stages when available. c, The Pearson correlation between the replicates (n = 2) of H3K4me3 for mouse pre-implantation embryos at each stage. d, Scatter plots showing the H3K4me3 enrichment levels (2-kb window) between replicates across the genome for mouse pre-implantation embryos at each stage. e, Scatter plot showing the H3K4me3 enrichment levels (2-kb window) in MII oocytes between data sets generated using an in-house antibody or a commercial antibody (Millipore 04-745). f, A snapshot of the UCSC browser view shows H3K4me3 STAR ChIP–seq results using two different H3K4me3 antibodies (in-house or commercial/Millipore 04-745) in mES cells and MII oocytes. Annotated genes and repetitive elements are also shown. g, Venn diagram showing the overlap between mES cell H3K4me3 (conventional ChIP–seq) promoter peaks and ICM H3K4me3 promoter peaks. h, Snapshots of the UCSC browser views showing the H3K4me3 and expression signals near Foxa1 (left), Atp1b1 (middle) and Tbx3 (right).
