FAQ: Do I need to spike in custom sequencing primers when sequencing libraries made with NEBNext® Multiplex Oligos for Enzymatic Methyl-seq on Illumina® sequencing instruments?

No. Libraries made using NEBNext Multiplex Oligos for EM-seq (96 Unique Dual Index Primer Pairs) are fully compatible with Illumina sequencing protocols for TruSeq® HT libraries. For HiSeq®, HiScan®SQ, or GAIIx systems on single-read flow cells, the TruSeq Dual Index Sequencing Primer Box, Single Read (single use box) (Illumina catalog # FC-121-1003) will need to be ordered separately when using both indices. This add-on box is not required with the MiSeq System or on paired-end flow cells for HiSeq, HiScanSQ, GAIIx. Please refer to the Illumina website for complete information.