Introducing the Illumina DNA/RNA UD Indexes

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

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

Sequence Updates The complete list of adapter sequences are provided in the updated Illumina Adapter Sequences Document #1000000002694. Indexes updated in the Illumina DNA/RNA UD Indexes kits will use the listed “v3” sequences where listed, and the “v2” sequences of UDP0252, UDP0258, UDP0289, UDP0290, UDP0291, and UDP0301. Please note, some “v2” index sequences have been moved to other plates to generate the “v3” indexes. (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 # 1000000041074.

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 and can produce Sample Sheets to export 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 Support 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).

Compatible Library Prep Kits

For any questions, contact Illumina Technical Support

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