Extended Data Fig. 5: aChIP data quality analysis for transcription factors and chromatin enzymes.
From: aChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs
a, Pearson correlation for two replicates of aChIP for RNAPII from 50 DPA rapeseed seeds, CAMTA3-FLAG, MBD7-MYC and DME-FLAG from Arabidopsis seedlings. 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. b, Motif prediction of the indicated CAMTA3-binding regions based on aChIP data. The identified motif was found in 15.2% of the target sequences, compared to 6.5% in the background sequences. The top 10 predicted motifs were shown. c, Bubble chart showing the top 7 enriched GO terms for genes associated with common CAMTA3-binding peaks and aChIP unique peaks, in comparison to rChIP data. The x-axis represents the ratio of the number of genes in the candidate set enriched in this GO term to the total number of genes in the background set involved in the same GO term. The y-axis lists the GO terms. Each bubble corresponds to a specific GO term. The color of each bubble signifies its statistical significance (p.adjust), calculated using the Benjamini & Hochberg method. The size of each bubble is proportional to the number of genes it includes, with larger bubbles indicating a higher gene count. d, Peak profiles displaying the distribution of CAMTA3-binding signals across aChIP unique peaks (± 2 kb) in the indicated categories. Wild-type (Col-0) FLAG ChIP-seq served as control. The peak region is converted into percentiles to standardize peaks of different lengths. e, Venn diagrams showing the overlap of MBD7-MYC peaks identified by aChIP and published data (Lang et al., 2015). f, Peak profiles displaying the distribution of MBD7-binding signals across aChIP unique peaks (± 2 kb) in the indicated categories. Wild-type (Col-0) MYC ChIP-seq served as control. The peak region is converted into percentiles to standardize peaks of different lengths. g, Barplots showing the genome distribution and proportion of DME binding regions.
