NEXTFLEX-96 ChIP-Seq Barcodes

  • Compatible with ChIP-seq® and very low input DNA-seq applications using NEXTFLEX® ChIP-Seq and NEXTFLEX® Rapid DNA-Seq 2.0 Kits
  • 8 nt index contained within adapter sequence
  • Considerably reduce your per-sample sequencing cost by barcoded multiplexing
  • Increase your sequencing scale by pooling several samples on a single flow cell
  • Customized plating options available
  • Compatible with Illumina® next-generation sequencing platforms

  • NOVA-514124


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

Increase Scale while Reducing Your Cost

The NEXTFLEX-96 ChIP-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 ChIP-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 caused by 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 ChIP-Seq Barcode index sequences are designed to have a hamming distance of 4, allowing discrimination of different barcodes even in the case of an error in the barcode read. These adapters, compatible with Illumina® platforms, are available in custom formats.

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

These barcodes can be used with single, paired-end, and multiplex reads and are compatible with the NEXTFLEX® Rapid DNA-Seq Kit 2.0 and the NEXTFLEX® ChIP-Seq Kits and other low input DNA-seq protocols.

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 recent blog post, Tech Tips – Barcode Recommendations for Low Level Multiplexing, to learn how to avoid registration failure on an Illumina® sequencer caused by lack of sufficient index sequence diversity.


  • NEXTFLEX-96 ChIP HT Adapter (0.6 µM)
  • NEXTFLEX® Primer Mix (12.5 µM)


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

Selected Publications that Reference Using the NEXTFLEX-96 ChIP-Seq Barcodes:

  • Derboven, E., Ekker, H., Kusenda, B., Bulankova, P., Riha K. (2014) Role of STN1 and DNA Polymerase α in Telomere Stability and Genome-Wide Replication in ArabidopsisPLoS Genetics. DOI: 10.1371/journal.pgen.1004682
  • Jiang, L. et al. (2014) ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells. PLoS ONE 9(4): e94187. doi: 10.1371/journal.pone.0094187
  • Thakur J. and Sanyal K. (Feb 2013) Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans. Genome Research. doi: 10.1101/gr.141614.112
  • Yamane A. et al. (2013) RPA Accumulation during Class Switch Recombination Represents 5′–3′ DNA-End Resection during the S–G2/M Phase of the Cell Cycle. Cell Reports.

The NEXTFLEX-96 ChIP-Seq Barcodes Kits contain 8 reactions each of 96 unique barcodes, enabling the user to multiplex up to 96 samples. This kit is shipped on dry ice.

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