Extended Data Fig. 5: Quality control for the SLAM PAS-seq.
From: Alternative polyadenylation by sequential activation of distal and proximal PolyA sites
a, Rates of nucleotide substitutions with or without DRB treatment. b, Relative T-C nucleotide conversion of mRNA and mitochondria RNA w/o DRB treatment. Data are presented as mean values ± SD (n = 2). c, Correlation coefficients of expression values in CPM between pairs of samples. total: total reads; new: nascent reads with T-C conversion. d, Difference of d/p ratios between the nascent RNA and steady state RNA. NM, NM&NP, NP, and others are different groups of genes with longer 3′UTR isoform enriched in the NM only, both NM and NP, NP only (groups as Fig. 1 g), non-enriched in neither NM nor NP (gray points in Fig. 1e,f), respectively. NP: nucleoplasm; NM: nuclear matrix. The p-values are based on a two-tailed unpaired t test. e, Scatter plot showing the d/p ratios of total RNA-seq with or without 4sU treatment in cell culture. f, Gene counts with different numbers of APA pairs using the most distal PAS as reference. g, Summary of genes classified by the d/p ratio of the nascent over steady state RNA of their APA pairs. h, Box plot showing the d/p ratios of total RNA is altered slightly upon transcription inhibition with DRB treatment. The dotted lines represent the value ±1. The lower and upper hinges of the boxplots correspond to the first and third quartiles (the 25th and 75th percentiles). The upper whisker extends from the hinge to the largest value no further than 1.5 * IQR from the hinge (where IQR is the interquartile range, or distance between the first and third quartiles). The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. The centre line represents the median value.