NEBNext^® Multiplex Oligos Selection Chart

NEBNext Multiplex Oligos for Illumina^®

• Index Primers Set 1
• Index Primers Set 2
• Index Primers Set 3
• Index Primers Set 4
• 96 Index Primers

• Dual Index Primers Set 1
• Dual Index Primers Set 2

• 96 Unique Dual Index Primer Pairs Set 1
• 96 Unique Dual Index Primer Pairs Set 2
• 96 Unique Dual Index Primer Pairs Set 3
• 96 Unique Dual Index Primer Pairs Set 4
• 96 Unique Dual Index Primer Pairs Set 5
• Unique Dual Index Primer Pairs for EM-seq™

• Unique Dual Index UMI Adaptors DNA Set 1
• Unique Dual Index UMI Adaptors DNA Set 2
• Unique Dual Index UMI Adaptors DNA Set 3
• Unique Dual Index UMI Adaptors DNA Set 4
• Unique Dual Index UMI Adaptors RNA Set 1

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 480

384 for DNA; 96 for RNA

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

Five; 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).

Four sets for DNA, One set for RNA; Adaptors with 96 indices in premixed, foil-sealed 96-well plate (DNA-seq or RNA-seq) and primers