The combinations below are selected for color balance, so that each index cycle has signal in every detection channel. They apply to 4-channel instruments (e.g., MiSeq), 2-channel instruments (e.g., NextSeq 550, NovaSeq 6000), and XLEAP-SBS instruments (NextSeq 1000/2000, NovaSeq X Series). Index numbers refer to the indexes included with each kit. In each combination, the DNA index is shown in bold.
Note: A single sample cannot be fully color balanced on 2-channel instruments. For single-sample or very low-plex runs, spike in PhiX or pool with other libraries as per Illumina's best practices.
Note: Sequencing Protein or RNA libraries alone is not recommended. These libraries have very low Read 2 diversity, which may cause sequencing issues. Sequence them together with DNA libraries or other high-diversity, non-Mission Bio libraries, or increase the PhiX spike-in.
DNA Only
DNA + RNA
DNA + Protein
DNA + RNA + Protein
*For 5+ samples on NextSeq 1000/2000 or NovaSeq X Series instruments, not all combinations are color balanced. Start from the 4-sample combination above and add samples with unique indexes; adding libraries to a balanced pool keeps it balanced.