Supplementary Figure 2: Inter-replicate concordance, quantitative PCR–validation data, and transcript-size distribution and expression analyses.

a) Concordance between RNA-Seq expression data from biological replicates (#1 and #2). Pearson correlation coefficients (r) are depicted above each graph. b) qPCR validation for a subset of B lineage specific lncRNA genes identified by RNA-Seq: Gene expression measured by RNA-Seq (mean expression from two biological replicates per cell type) and qPCR (from an additional biological replicate separate to those used for RNA-Seq). Pearson correlation coefficients (r) between measurements from the two methods are depicted at left. Additional qPCR reactions for the same genes using one of the replicates used for RNA-seq showed similar results (not shown). (c) Size distribution of novel lncRNA transcripts. Data for transcripts from protein coding and annotated lncRNA databases are depicted for comparison. (d) Violin plot of transcript expression levels (mean, standard deviation, range). For each transcript, the maximum expression value (among 20 samples) was used for the plot. Class 1- transcripts from annotated lncRNA genes that lack novel isoforms; class 2- annotated transcripts from lncRNA genes that have both novel and annotated isoforms; class 3- novel transcripts from annotated lncRNA genes; class 4- transcripts from novel lncRNA genes. Expression levels were higher for novel lncRNA transcripts than for annotated lncRNA transcripts.