Advantages of RNA-seq gene expression compared with microarrays
In planning a gene expression experiment, most people start thinking about how many microarrays they will need to order for their project. While arrays have been a standard and reliable technology for gene expression experiments in the past, next generation sequencing methods are surpassing hybridization techniques in popularity. Check out these articles in PlosOne and The Scientist for more information on the benefits of RNA-seq for gene expression. The benefits of RNA-seq expression include:
- Increased sensitivity and specificity
- Elimination of errors and signal noise that are common for hybridization based experiments
- Improved sensitivity to detect rare and low abundance transcripts
- Provides absolute transcript counts, instead of relative expression levels.
But conventional RNA-seq can be costly and difficult for non-experts to analyze.
That is where Targeted RNA-seq comes in.
Most gene expression projects prioritize assessment of protein-coding genes. Targeted RNA-seq can use either large amplicon panels or 3′ polyadenylated transcript selection to target the mRNA genes you are interested in comparing. Because this represents a small portion of the transcriptome, more samples can be sequenced at higher depth compared to whole transcriptome. In addition, as there is only one count per transcript, the data is simple to analyze without the need for transcript length normalization. Want another reason to try targeted RNA-seq? It also works on mildly to moderately degraded RNA extracted from formalin-fixed paraffin embedded samples.
For sample preparation choose from:
IonAmpliseq Human Gene Expression Kit targeting over 20,000 genes
IonAmpliseq MouseGene Expression Kit targeting over 23,000 genes
Lexogen Quant-seq 3′ mRNA-Seq Library Prep Kits to provide gene expression analysis for human and non-human targets (any species with polyadenylated transcripts).