Fig. 1

Four platforms. a NanoString nCounter. A capture probe works together with a reporter probe to capture the signal in the target sequences. Each capture-reporter probe pair is tagged with a distinct color-coded barcode to represent the detection of a single target molecule for direct digital readout. nCounter Digital Analyzer reports the expression levels of targeted mRNAs. In this example, Probe 1 measures the total expressions of all the isoforms of the gene; Probe 2 measures the expression of Isoform 1; Probe 3 measures the expression of Isoform 3. b mRNA-sequencing (RNA-seq). Paired-end sequencing of fragmented cDNAs generated by next-generation sequencing technology are aligned to the reference genome. The read coverage can be analyzed to infer the mRNA abundance by RNA-seq quantification methods. c Exome Microarray. In the Microarray experiment, exon-level expressions are estimated based on the hybridization intensity measurements by multiple probes targeting the putative exonic regions. After normalization, quantification methods are applied to estimate gene and isoform expressions. d Quantitative reverse transcription PCR (RT-qPCR). In this platform, RNAs are first transcribed into cDNAs by reverse transcriptase from the total RNA. Then the cDNAs are used as the template for the qPCR reaction. The gene and isoform expression can be estimated based on the amplified DNAs after performing qPCR