A large-scale comparative study of isoform expressions measured on four platforms

The NanoString experiment were conducted on 59 cell lines including 12 ovary cell lines, 12 lung cell lines, 11 colon cell lines, 10 breast cell lines, 4 pancreas cell lines, 2 prostate cell lines, 2 stomach cell lines, and 6 cell lines of 6 other types of tissues. A total of 404 probes were customized to estimate the isoform expressions of 155 cancer genes curated from the literature with more reliable isoform annotations, where each of the 155 gene contains at least two isoforms. RT-qPCR data on seven genes in twelve out of the 59 cancer cell lines are available at https://github.com/compbiolabucf/IntMTQ/tree/master/RT-qPCR We worked with NanoString Technologies to design an experiment for measuring the isoform expressions of 155 multi-isoform cancer genes in 59 cell lines. 79 genes contain two isoforms, 37 genes contain three isoforms, 18 genes contain four isoforms, and 21 genes contain more than four isoforms. We customized 404 capture-reporter probes to capture the 478 isoforms expressions in the genes. In addition, 14 probes for quality control and 10 spike-in probes for measuring 10 house keeping genes for normalization of the data are also introduced. Each probe is 100 bps long designed to capture a target sequence in one or multiple isoforms. For each gene, the probes were designed to best distinguish the expressions of all the isoforms in the gene, and one of the probes was always designed to measure the gene expression.