Figure 5 : Differentially expressed genes in ribo-depleted and poly-A–enriched libraries.

From: Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

Figure 5

(a) The percentage of reads that map to various gene sequence categories. There were more intronic reads from ribo-depleted than poly-A–enriched libraries. The sequence type and read distribution of gene features detected in poly-A–enriched and ribo-depleted libraries from the same sample were examined using GENCODE (v12) annotations. Mitochondrial RNA reads are present at trace levels (<0.1%, data not shown). (b) Differentially expressed genes (DEGs) were detected in all pairwise comparisons of the original (A, B) and mixed samples (C, D); (c) results were similar for both library types from the common set of detected genes at all fold-change (FC) and false discovery rate (FDR) thresholds tested. (d) Both library types show similar accuracy as evidenced by Matthews Correlation Coefficients (MCC) with RT-qPCR assays (see Supplementary Fig. 29b for expanded data). A subset of GENCODE mapped reads was used from each library (mean = 37.6 × 106 reads per replicate, s.d. = 2.07 × 106) to ensure the same number of exon-mapped reads per sample was compared between all replicates.