NEXTFLEX-96 RNA-Seq Barcodes

  • Index contained within adapter sequence eliminates the need to perform PCR to add flow cell binding sequences
  • Multiplex up to 96 libraries
  • Considerably reduce your per-sample sequencing cost by barcoded multiplexing
  • Increase your sequencing scale by pooling 100s of samples on a single flow cell
  • Compatible with Illumina® next-generation sequencing platforms
  • Compatible with the NEXTFLEX® Rapid RNA-Seq Kit and the NEXTFLEX® Rapid Directional RNA-Seq Kit
  • Not compatible with the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0

  • NOVA-512915


    (in 96-well plate)
    768 rxns
Download Manual
For research use only. Not for use in diagnostic procedures.

Increase Scale while Reducing Cost

The NEXTFLEX-96 RNA-Seq Barcodes are adapters that were designed for use with the NEXTFLEX® Rapid RNA-Seq Kit and the NEXTFLEX® Rapid Directional RNA-Seq Kit. These barcodes are not recommended for use with the new NEXTFLEX® Rapid Directional RNA-seq kit 2.0.

The NEXTFLEX-96 RNA-Seq Barcodes can be used to provide flexibility and high-throughput capabilities in sequencing applications. They significantly increase scale while reducing costs by allowing the user to pool multiple library preparations in a single flow cell lane. The NEXTFLEX-96 RNA-Seq Barcodes kits accomplish this by using an indexed adapter with an 8 nt unique sequence. This allows for proper differentiation between samples, preventing poor reads from single base errors introduced during PCR. The NEXTFLEX® index is contained within the adapter sequence eliminating the need to perform PCR to add flow cell binding sequences. The NEXTFLEX-96 RNA-Seq Barcode index sequences are designed to have a hamming distance of 4, allowing discrimination of different adapters even in the case of an error in the barcode read. These adapters are supplied a 96-well format.

Do you want to index you samples but don’t want to use 96 different barcodes? We also offer the NEXTFLEX® RNA-Seq Barcodes in sets of 6, 12, 24 and 48 barcodes.

For larger volume requirements, customized and bulk packaging is available. Please contact [email protected] for further information.

Avoiding Registration Failure with Low Level Multiplexing

Registration failure could occur if the color balance was not maintained between the red and green lasers (used to sequence A/C bases and G/T bases, respectively). Read our blog post, Tech Tips – Barcode Recommendations for Low Level Multiplexing, to learn how to avoid registration failure on an Illumina® sequencer caused by lack sufficient index sequence diversity.


  • NEXTFLEX® RNA-Seq Barcode Adapter (0.6 µM)
  • NEXTFLEX® Primer Mix (12.5 µM)


  • Sequences of NEXTFLEX RNA-Seq Barcode Indexes – Excel / PDF
  • Sequences of NEXTFLEX-96 RNA-Seq Barcode Indexes – Excel / PDF

Selected Publications that Reference using the NEXTFLEX-96 RNA-Seq Barcodes

  • Harvey, C. T. et al. (2015) QuASAR: quantitative allele-specific analysis of reads. Bioinformatics. Doi: 10.1093/bioinformatics/btu802
  • Moyerbrailean, G. A., et al. (2015) A high-throughput RNA-seq approach to profile transcriptional responses. Scientific Reports. 5: 14976. doi: 10.1038/srep14976.
  • Takashima, Y. (2014) Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human. Cell. 158: 6, 1254–1269.

The NEXTFLEX-96 RNA-Seq Barcodes Kits contain 96 unique adapters compatible with Illumina® platforms, enabling the user to multiplex up to 96 RNA-seq samples. These kits ship on dry ice.

These barcodes are not recommended for use with the new NEXTFLEX® Rapid Directional RNA-seq kit 2.0. For early access evaluations of this kit, 8 reactions of barcodes will be provided at no cost.

Alternative Solutions:

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