Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
Clark MB., Mercer TR., Bussotti G., Leonardi T., Haynes KR., Crawford J., Brunck ME., Cao K-AL., Thomas GP., Chen WY., Taft RJ., Nielsen LK., Enright AJ., Mattick JS., Dinger ME.
We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas.