<p><span style="font-size:14px">RNA-seq&nbsp;(RNA sequencing), also called&nbsp;whole transcriptome shotgun sequencing<span style="line-height:17.3333px">,&nbsp;</span>uses next-generation sequencing&nbsp;to reveal the presence and quantity of RNA&nbsp;in a biological sample at a given moment in time.&nbsp;RNA-Seq is used to analyze the continually changing cellular transcriptome.&nbsp;Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations, SNPs and&nbsp;changes in gene expression.<span style="line-height:17.3333px">&nbsp;</span>In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA and ribosomal profiling.&nbsp;RNA-Seq can also be used to determine exon/intron&nbsp;boundaries and verify or amend previously annotated 5&rsquo; and 3&rsquo; gene boundaries.&nbsp;Prior to RNA-Seq, gene expression studies were done with hybridization-based microarrays.&nbsp;Issues with microarrays include cross-hybridization artifacts, poor quantification of lowly and highly expressed genes, and the knowledge of the sequence.<span style="line-height:17.3333px">&nbsp;</span>Because of these technical issues, transcriptomics transitioned to sequencing-based methods. These progressed from Sanger sequencing of Expressed Sequence Tag&nbsp;libraries, to chemical tag-based methods&nbsp;and finally to the current technology, NGS of cDNA.&nbsp;</span></p>