Get Help Sign In
Icons Library_Wave_180x180_CRISPR

rhAmpSeq™ Index Primers

Combine amplicon libraries in a single sequencing run for maximum efficiency

Use rhAmpSeq Index Primers to prepare amplicon libraries for targeted sequencing on Illumina® platforms by adding a unique, identifying “barcode” sequence to each amplicon. Request exactly the primers you need from the 96 sample indexes available for P5 and P7 Illumina® index primer sequences. IDT scientists have tested and validated these 96 sample index sequences to ensure optimal performance.


rhAmpSeq Index Primers

Add unique "barcode" sequences and P5/P7 sequences to your amplicon libraries. Priced per primer.

Product details

rhAmpSeq Index Primers are used in the second amplification step of the rhAmpSeq workflow, Indexing PCR 2, to add both unique index sequences and the P5/P7 sequences recognized by Illumina® sequencing instruments (Figure 1). These 96 index sequences are available for both the P5 and P7 primers. Adding these sequences to the amplicons created in the first amplification step, Targeted rhAmp PCR 1, creates dual-indexed libraries.

IDT scientists designed and tested the 96 index sequences for optimum performance.

Figure 1. Detail of amplification steps in the rhAmpSeq workflow. RNase H2 activates rhAmp primers by target-specific cleavage of the RNA base within the DNA:RNA duplex, removing a 3′ blocker. RNase H2 activity is highly specific, thus reducing the amount of amplification from non-specific hybridization and primer dimers. Only activated rhAmp primers can be extended to generate target amplicons.

Illumina® sample barcodes and P5/P7 sequences are incorporated during Indexing PCR 2.

System features and specifications

Supported applications/protocols

On- and off-target analysis of genome editing experiments

High-throughput analysis of on-target genome editing experiments

Insert sizeFlexible (50–200 nt)
Custom panel sizeUp to 5000 amplicons per panel
Sample indexing capability96 index sequences (up to 9216 combinations)
Compatible platformsIllumina®
Hands-on time*1–1.5 hr
Data analysis time**0.5–2 hr

* Estimated time to process 12–96 samples using manual pipetting, including reaction setup, cleanup, library quantification, and normalization steps
** Estimated time to process sequencing data (up to 500 amplicons) through rhAmpSeq CRISPR Analysis Tool


Frequently asked questions