RNA-seq is the technique used to learn about gene expression differences at the transcriptome level. It works better than many genome sequencing methods because the mRNAs are much smaller and no or little alignment is needed.

The first step is to create a cDNA library often times through a poly A tail search using magnetic beads. Once the library is created the sequencing is able to happen using high throughput technology.

This technique is used in many cancer tissue assays where researchers want to know the differences in total gene expression (all genes) between cancerous and non cancerous tissue (or between different stages).

454 Sequencing [10] Illumina [11] SOLiD [12]
Sequencing Chemistry Pyrosequencing Polymerase-based sequence-by-synthesis Ligation-based sequencing
Amplification approach Emulsion PCR Bridge amplification Emulsion PCR
Paired end separation 3 kb 200 bp 3 kb
Mb per run 100 Mb 300 Gb 3000 Mb
Time per paired end run 7 hours 7–14 days 5 days
Read length (update) 250 bp (400 bp) 100 bp (50-100 bp) 35 bp (35-50 bp)
Cost per run $ 8,438 USD $ 11,750 USD $ 17,447 USD
Cost per Mb $ 84.39 USD $ 1.00 USD $ 5.81 USD

This table is from the wikipedia page here and is a helpful guide as to which sequencing platform may be best for your study.