PerkinElmer NEXTflex Rapid Directional qRNA-Seq

PerkinElmer NEXTflex Rapid Directional qRNA-Seq


  • Generates stranded, molecular indexed RNA-Seq libraries
  • Enables high precision, quantitative measurement of RNA expression
  • Enhanced Adapter Ligation Technology offers a larger number of unique sequencing reads
  • Input 10 ng – 1 µg total RNA for enrichment by NEXTFLEX® Poly(A) Beads or ~ 1 ng – 100 ng isolated mRNA or rRNA-depleted RNA
  • Embedded sample index barcodes for multiplexing of up to 96 samples
  • Automation protocols are available for the Sciclone® NGS and NGSx Workstations
  • Functionally validated with Illumina® sequencing platforms
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Image Variation SKU Price Quantity Add To Cart
8 Rxn Barcode 1 4 - NOVA-5130-01D 1,375.00
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48 Rxn Barcodes 1 24 - NOVA-5130-02D 7,400.00
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48 Rxn Barcodes 25 48 - NOVA-5130-03D 7,400.00
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The patent pending NEXTFLEX® Rapid Directional qRNA-Seq Kit enables high precision directional gene expression analysis by RNA-Seq from 10 ng – 100 ng mRNA or rRNA-depleted RNA or 10 ng – 10 µg total RNA for enrichment by NEXTFLEX® Poly(A) Beads. Developed in conjunction with Cellular Research Inc., this kit generates directional RNA-Seq libraries equivalent to conventional stranded RNA-Seq libraries, but with the added feature of molecular indexing. The NEXTFLEX® Rapid Directional qRNA-Seq Kit can be used to obtain stranded information which identifies the specific DNA strands a given RNA transcript was derived from allowing for proper detection of antisense and ncRNA expression.

Molecular Labeling of Individual RNA Molecules

The NEXTFLEX® Rapid Directional qRNA-Seq Kit contains a set of 96 distinct molecular labels on the sequencing adapters. Each label consists of an 8 nucleotide barcode tag. During the ligation reaction, each cDNA fragment independently and randomly ligates to a single label from this pool of 96 adapters to result in a total of 96 x 96 = 9,216 possible combinations across both ends. For every clone sequenced, paired-end reads reveal the chosen label on each end along with adjoining cDNA sequence. This allows for differentiation between re-sampling of the same molecule and sampling of a different molecule of identical sequence. Analysis using molecular indexing information provides an absolute, digital measurement of gene expression levels, irrespective of common amplification distortions observed in many RNA-Seq experiments. In addition to encoding cDNA fragments at the molecular level, the kit also allows for the application of sample-specific barcodes during the library preparation PCR step. A more detailed description of the use of molecular indexing for stranded RNA-Seq is available in our product application note.


The NEXTFLEX® Rapid Directional qRNA-Seq Kit, mRNA or rRNA-depleted RNA is fragmented using a cationic buffer. Fragmented RNA undergoes first and second strand synthesis, followed by adenylation, ligation and PCR. This kit incorporates the NEXTFLEX® Rapid Reverse Transcriptase, a robust, thermostable RT that outperforms other RTs on the market for NGS applications.

Stranded RNA-Seq Automation Protocols Available

Optimized automation protocols for stranded RNA library prep using the NEXTFLEX® Rapid Directional qRNA-Seq Library Preparation Kits are available for the Sciclone® NGS and NGSx Workstations. These protocols are designed to facilitate higher sample throughput, less hands-on time, greater reproducibility and improved process control.

The NEXTFLEX®  Rapid Directional qRNA-Seq Kit contains enough material to prepare 8 or 48 RNA samples for Illumina® compatible paired end sequencing. The shelf life of all reagents is 12 months when stored properly. All components can safely be stored at -20°C.

Additional information


8 rxn Barcode 1-4, 48 rxn Barcodes 1-24, 48 rxn Barcodes 25-48




  • Sequences of NEXTFLEX Rapid Directional qRNA-Seq Barcoded Primers Indexes – Excel / PDF
  • Sequences of NEXTFLEX Rapid Directional qRNA-Seq  Molecular Indexes A1 – A96 – Excel / PDF

qRNAseq STL Script for Accurate Molecular Quantification of mRNA Transcription with Molecular Indexes™

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