NEBNext® Multiplex Oligos Selection Chart

 

SINGLE INDEX

DUAL INDEX

UNIQUE DUAL INDEX

UNIQUE DUAL INDEX UMIs

NEBNext Multiplex Oligos for Illumina®

Contains UMI

No

No

No

Yes

Addresses index hopping

No

No

Yes

Yes

Indexing Strategy

Index Primer

Index Primer

Index Primer

Index Adaptor

Applications

DNA-seq, RNA-seq 
(except Small RNA)

DNA-seq, RNA-seq
(except Small RNA)

DNA-seq, RNA-seq
(except Small RNA)

PCR-free DNA-seq, RNA-seq 
(except Small RNA)

Number of indices  for multiplexing

up to 144

up to 384

up to 384

up to 96

Compatible with ARTIC sequencing for Illumina
Yes Yes  Yes No

Compatible with EM-seq

Yes*

Yes*

Yes*

No

Compatible with EpiMark® bisulfite sequencing

Yes**

Yes**

Yes**

No

Number of sets available; formats and indices available

Five; Sets 1-4 (12 indices/set): Individual vials 96 Index: Premixed plate

Two; individual vials containing 8 i5 primers and 12 i7 primers for combinatorial mixing

Four; 96 indices in premixed, foil-sealed 96-well plates; Including a version for EM-seq (up to 120 indices, either 96-well plate or 24 vial format).

One; 96 indices in premixed, foil-sealed 96 well plate (DNA-seq OR RNA-seq) and primers

* Requires the use of the EM-seq Adaptor; Single, dual and unique dual index are all compatible; NEB recommends using the Unique Dual Index Primers found in the NEBNext Enzymatic Methyl-seq Kit (NEB #E7120) or the NEBNext Multiplex Oligos for EM-seq (NEB #E7140), both supplied with the NEBNext EM-seq Adaptor; For higher levels of multiplexing, Unique Dual Index Primers Sets 3 and 4  (NEB #E6444 and #E6446) are also validated for EM-seq.

**  Requires use of NEBNext EM-seq adaptor from NEBNext Multiplex Oligos for Enzymatic Methyl-seq (Unique Dual Index Primer Pairs, #E7140S/L or NEBNext methylated adaptor from NEBNext Multiplex Oligos for Illumina® (Methylated Adaptor, Index Primers Set 1, #E7535S/L) .