Fig. 1: ABC singleplex evaluation.
From: Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP
a, Schematic of ABC and eCLIP workflows. Yellow blocks highlight differences between the two protocols. b, Genome browser tracks showing binding sites of RBFOX2 and SLBP for duplicate ABC and eCLIP experiments. Each panel is group-normalized by RPM value. Replicate RBFOX2 data were generated in HEK293XT cells and SLBP data were generated from K562 cells. c, Percentage of uniquely mapped reads that are within eCLIP IDR peaks (top) for two replicates. Percent of reads mapping to conserved GCAUG sites (bottom). d, Significant peaks of ABC and eCLIP replicate 1 (P < 0.001 and greater than eightfold change) in RBFOX2-dependent skipped exon events, defined as exons alternatively included/excluded upon RBFOX2 shRNA KD12 (*P < 0.05, **P < 0.001; ***P < 10-4 with two-sided chi-squared test). e, Percent of uniquely mapped reads that map to histone mRNAs in eCLIP and ABC libraries, for duplicates, shown separately. f, Mean relative information content of reads (IP versus SMI for eCLIP; IP versus RNA-seq for ABC) from ABC or eCLIP across all histone mRNAs. Error bar represents standard error across all histone genes. g, Cumulative count of histone genes across the top 100 ranked genes based on two-sided enrichment P value.
