Unbiased exploration of gene expression

Key applications of RNAseq

RNA sequencing (RNAseq) provides unbiased, specific, and sensitive quantification of coding and non-coding RNA transcripts, as well as alterations such as splice variants, gene fusions, mutations, and RNA editing events.

RNAseq is the preferred method for numerous clinical applications including:

  • Gene signature discovery
  • Molecular characterization of tumors
  • Elucidation of disease mechanisms or discern patient subgroups
  • Study of drug mode of action

Our RNAseq expertise

CellCarta leverages the power of next generation sequencing (NGS) by using the NovaSeq 6000, NextSeq 550Dx, and MiSeq platforms. Our offering spans from RNA extraction, library preparation, sequencing, to data analysis and reporting.

To further support your findings, we provide orthogonal result validation using quantitative and digital PCR. Depletion of unwanted small RNA molecules from the total RNA investigated is also offered.

Our customized RNA sequencing workflow

For targeted gene expression studies for specific mRNA, microRNA or lncRNA genes or gene panels, off-the-shelf assays for almost all genes are available. We also offer numerous gene expression panels (mRNA, microRNA and lncRNA) for a broad range of pathways and disease states. For genes where no off-the-shelf assay is available, assays can be developed with custom primers.

Application Library kit used
polyA mRNA TruSeq® Stranded mRNA Library Prep (Illumina®)
small RNA NEBNext® Multiplex Small RNA Library Prep Kit for Illumina®
RNA capture TruSeq® RNA exome library (Illumina®) RNA Prep with Enrichment, (L) Tagmentation kit (Illumina®)
High-throughput RNAseq QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina®
Total RNA SMARTer® Stranded Total RNA-Seq Kit (Takara Bio)
Custom Capture Design of custom capture probes with Twist Biosciences capture reagents


Based on your sequencing needs, our team can develop customized sequencing workflow which can be applied to various sample types (fresh tissue, fresh frozen tissue, fixed tissue, body fluids, whole blood, cells).

Optimized high-throughput RNAseq for pre-clinical compound screening

Get insights on the mode of action underlying induced cellular phenotypes, reveal potential compound-induced toxicities or off-target effects, and compound similarities with our high throughput molecular cellular phenotyping service.

To bridge the demand between expression data of genes for a few samples by classic RNA sequencing and for thousands of samples at low cost by qPCR, our team developed a high-throughput shallow 3’ RNA sequencing method using crude cell lysates. The workflow can process up to 384 cell lysates without the need for RNA extraction. Data is shared through Savanna, our proprietary data visualization app to help you visualize and compare data points.

The method can also be used to characterize therapeutic molecules, including small molecules and RNA targeting agents such as siRNAs and antisense oligonucleotides (ASO).

Contact us to learn more about our high throughput RNAseq services for pre-clinical compound screening

RNA profiling for liquid biopsies

RNA profiling has emerged as a powerful tool to investigate the biomarker potential of human biofluids. Our team published an RNA sequencing method using a dedicated RNA library kit to properly quantify extracellular RNA content and provide the complete transcriptome of a wide range of biofluids.

Learn more