Summary of RNA sequencing.

<p>Within the organisms, genes are transcribed and spliced (in eukaryotes) to produce mature mRNA transcripts (red). The mRNA is extracted from the organism, fragmented and copied into stable double-stranded–cDNA (ds-cDNA; blue). The ds-cDNA is sequenced using <a href="http://en.wikipedia.org/w/index.php?title=DNA_sequencing#High-throughput_methods" target="_blank">high-throughput</a>, short-read sequencing methods. These sequences can then be <a href="http://en.wikipedia.org/w/index.php?title=Sequence_alignment" target="_blank">aligned</a> to a reference genome sequence to reconstruct which genome regions were being transcribed. These data can be used to annotate where expressed genes are, their relative expression levels, and any alternative splice variants.