Figure 1 : Using the CLS approach to extend GENCODE lncRNA annotation.

From: High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

Figure 1

(a) The strategy for automated, high-quality transcriptome annotation. CLS can be used to complete existing annotations (blue) or to map novel transcript structures in suspected loci (gold). Capture oligonucleotides (black bars) are designed to tile across targeted regions. PacBio libraries are prepared for from the captured molecules. Illumina HiSeq short-read sequencing can be carried out for independent validation of predicted splice junctions (SJ). Predicted transcription start sites can be confirmed by CAGE clusters (green), and transcription termination sites by non-genomically encoded polyA+ sequences in PacBio reads (red). Rectangles with lighter shading and dashed outlines denote novel exons. (b) A summary of the human and mouse capture library designs. The numbers of individual gene loci probed are shown. PipeR pred., ortholog predictions in mouse genome of human lncRNAs made by PipeR29; snRNA, small nuclear RNA; snoRNA, small nucleolar RNA; UCE, ultraconserved elements; Prot. coding, expression-matched, randomly selected protein-coding genes; ERCC, spike-in sequences; Ecoli, randomly selected Escherichia coli genomic regions (enhancers and UCEs were probed on both strands, and these were counted separately). (c) Types of RNA samples used in the study.