Extended Data Fig. 2: Schematic diagrams for eChIP method, along with quality and efficiency analysis for aChIP data in rapeseed seeds.
From: aChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs
a, Schematic overview of eChIP. The eChIP method starts by fixing tissue with formaldehyde, followed by grinding tissues into fine powder, and subsequent homogenate lysis using buffer S. Then, the chromatin is fragmented and retained in the supernatant with buffer F, followed with IP (immunoprecipitation) with antibodies, ChIP-DNA purification and library sequencing. b, c, Observation and quantification of differences in cell nucleus count before the sonication step in the aChIP and rChIP methods. Cell nuclei were stained with DAPI. Each value represents the mean ± standard error of mean (n = 3 biological replicates). d, Comparison of signal-to-noise ratio based on the FRiP for H3K4me3 and H3K27me3 ChIP-seq datasets in 50 DPA (days post anthesis) rapeseed seeds. The dashed line indicated an FRiP of 30%. e, Pearson correlation for two replicates of H3K4me3 aChIP. Each point represents the log2 of mapped reads within the combined peaks of the two replicates. The R value calculated by Pearson correlation coefficient at the combined peaks is shown. f, Correlations of log2-fold-change in H3K4me3 and H3K27me3 (x-axis) and gene expression (y-axis) between 50 DPA seeds and young leaves. g, Genome browser screenshot showing H3K27me3 and H3K4me3 aChIP data for 50 DPA rapeseed seeds.
