Information on the Illumina DNA/RNA UD Indexes

Illumina has launched the Illumina DNA/RNA UD Indexes and the Illumina RNA UD Indexes, replacements for the IDT for Illumina DNA/RNA UD Indexes and the IDT for Illumina RNA UD Indexes, respectively. The latter have been obsolesced with a last order date of January 30, 2025. Note the “IDT for” naming is removed in the newer products.

Some of the indexes have been versioned to improve consistency and performance. Illumina has also optimized the plate arrangements to improve color balance.

Sequence Updates The complete list of adapter sequences are provided in the updated Illumina Adapter Sequences Document, "Illumina Unique Dual Indexes" section. Indexes updated in the Illumina DNA/RNA UD Indexes kits will use "v3" sequences where listed, and the "v2" sequences of UDP0252, UDP0258, UDP0289, UDP0290, UDP0291, and UDP0301. Note, some "v2" index sequences have been moved to other plates to generate the "v3" indexes kits. In contrast, IDT for Illumina DNA/RNA UD Indexes use "v2" sequences, where listed.

Plate Layouts Plate layouts are provided in the Index Adapters Pooling Guide.

Schematic of the index changes:

Usage Notes

• Due to the relocation of some indexes across plates,Illumina does not recommend combining IDT for Illumina DNA/RNA UD Indexes with the new Illumina DNA/RNA UD Indexes in the same run. This will avoid read misidentifications during sequencing analysis.

• BaseSpace Run Planning has been updated to include the new Illumina DNA/RNA UD Indexes to set up runs or allow for export of Sample Sheets for use with BCL Convert software.

• New Library Prep kit and Index kit definition files for use with Local Run Manager v2 and Local Run Manager v3 are available on the Illumina DNA/RNA Unique Dual Indexes Product Files page.

Catalog number changes

The IDT-ILMN RNA Index Anchors Box 96 (Catalog 20040899) subcomponent has not changed or been updated in the new Illumina RNA UD Indexes Set A-D, Ligation (96 Indexes, 96 Samples) (Catalogs 20091655, 20091657, 20091659, and 20091661). The RNA Anchor plate is required for Illumina Stranded RNA workflows and is only sold with the Illumina RNA UD Indexes, Ligation kits.

Compatible Library Prep Kits

For any feedback or questions regarding this article (Illumina Knowledge Article #8384), contact Illumina Technical Support [e-mail].