Targeted RNA-seq: a more sensitive and cost effective approach to gene expression analysis.

Gene Expression Profiling 

Gene expression profiling is one of the best ways to assess differences in cell populations or effects of an intervention in a cell population. Gene expression can be profiled using many different strategies. For global gene expression projects, sequencing of all the RNA transcripts, i.e. whole transcriptome sequencing, provides the most comprehensive assessment of RNA transcripts in a given cell or cell population. But it can be costly. And it requires sophisticated bioinformatic analysis. For investigators who are primarily interested in gene expression of protein coding genes, whole transcriptome may not be the most cost-effective tool. 

Targeted RNA-seq

Targeted RNA-seq is a sensitive, cost-effective technique for measuring gene expression of protein coding genes. Using amplicon panels or  3′ polyadenylated transcript selection, you can target the mRNA messages 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. 

Benefits of Targeted RNA-seq expression include:

Increased sensitivity and specificity over microarrays

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

Lower cost than whole transcriptome

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). 


ResourcePath will deliver:

  • Raw data BAM files
  • QC analysis
  • An excel file of normalized transcript counts

Turn around time:  5-7 days of receipt of RNA.

The excel file will be ready to upload into your favorite gene expression analysis program. Or, if you prefer, we partner with an expert bioinformatician who can help you make the most out of your data. 

Contact us to learn about RNA-seq gene expression