Illumina UD Indexes

Unique dual (UD) indexes enable preparation of high-quality libraries that can be multiplexed for increased throughput and cost-saving benefits.

January 30, 2025 is the last date IDT Illumina DNA/RNA UD Indexes Sets A–D (Catalog nos. 20027213, 20027214, 20042666, and 20042667) and IDT for Illumina RNA UD Indexes Sets A–D (Catalog nos. 20040553, 20040554, 20040555, and 20040556) will be available for order. 

We recommend transitioning to the Illumina DNA/RNA UD Indexes Sets A–D (Catalog nos. 20091654, 20091656, 20091658, and 20091660) and Illumina RNA UD Indexes Sets A–D (Catalog nos. 20091655, 20091657, 20091659, and 20091661). 

Overview

Illumina UD Indexes enable sequencing of significantly more samples per run without compromising data quality.

Key features

  • Decreases sequencing cost by multiplexing with 384 unique dual indexes (UDIs)

  • Minimizes the level and effect of index hopping

  • Enhances demultiplex accuracy during analysis

  • Increases throughput by simultaneously sequencing multiple samples in a single run

Expanding capabilities

The use of UDIs during library preparation for multiplexing ensures the most accurate demultiplexing and sequencing across Illumina sequencing platforms. To meet the needs of customers, Illumina offers UDIs to expand both instrument and library prep kit compatibilities.


Specifications


Required products

Library prep, enrichment, and probe panel reagents need to be ordered separately.

Compatible library prep kits:
Illumina RNA UD Indexes Set A-D and IDT for Illumina RNA UD Indexes Set A-D

  • Illumina Stranded Total RNA Library Prep
  • Illumina Stranded mRNA Library Prep

Illumina DNA/RNA UD Indexes Set A-D and IDT for Illumina DNA/RNA UD Indexes Set A-D

  • Illumina DNA Prep
  • Illumina DNA Prep with Enrichment
  • Illumina DNA PCR-Free Prep
  • Illumina RNA Prep with Enrichment
  • Illumina RNA Prep
  • Nextera XT DNA Library Preparation Kit

IDT for Illumina TruSeq RNA UD Indexes v2

  • TruSeq Stranded mRNA
  • TruSeq Stranded Total RNA

IDT for Illumina TruSeq DNA UD Indexes v2

  • TruSeq DNA Nano
  • TruSeq DNA PCR-Free
/ Results

Figures

Unique dual indexing has completely unique indexes

Resources

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Insights into index hopping | Illumina webinar

Gary Schroth, PhD gives an introduction to index hopping, explains how to minimize index hopping levels by following library prep best practices, and discusses how to remove index-hopped reads using unique dual indexing combinations.

Unique dual indexes reduce per-sample cost and sequence libraries with the highest accuracy compared to other indexing strategies.

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Sequencing: Introduction to sequencing by synthesis (SBS)

Explore the Illumina sequencing workflow in 3-dimensional detail. Go from sample preparation to cluster generation, sequencing on a flow cell with the proprietary SBS process, and data analysis.

Tips and best practices to avoid sequencing read misalignment associated with index switching.

Index adapters (18)

Illumina® RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples)

20091655

Illumina® RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep reagents separately.

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Illumina® RNA UD Indexes Set B, Ligation (96 Indexes, 96 Samples)

20091657

Illumina® RNA UD Indexes Set B, Ligation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep reagents separately.

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Illumina® RNA UD Indexes Set C, Ligation (96 Indexes, 96 Samples)

20091659

Illumina® RNA UD Indexes Set C, Ligation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep reagents separately.

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Illumina® RNA UD Indexes Set D, Ligation (96 Indexes, 96 Samples)

20091661

Illumina® RNA UD Indexes Set D, Ligation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep reagents separately.

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Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

20091654

Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

20091656

Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

20091658

Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

20091660

Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples) Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples)

20040553

Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep and probe panels separately.

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IDT® for Illumina® RNA UD Indexes Set B, Ligation (96 Indexes, 96 Samples)

20040554

Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep and probe panels separately.

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IDT® for Illumina® RNA UD Indexes Set C, Ligation (96 Indexes, 96 Samples)

20040555

Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep and probe panels separately.

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IDT® for Illumina® RNA UD Indexes Set D, Ligation (96 Indexes, 96 Samples)

20040556

Includes 96, 10 bp indexes sufficient for labeling 96 samples and RNA Index Anchor plate. Used with Illumina Stranded Total RNA Prep and Illumina Stranded mRNA Prep Kits. Purchase library prep and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

20027213

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

20027214

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

20042666

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT® for Illumina® DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

20042667

Includes 96, 10 bp indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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IDT for Illumina – TruSeq RNA UD Indexes v2 (96 Indexes, 96 Samples)

20040871

Includes 96, 8 bp indexes sufficient for labeling 96 samples and is compatible with TruSeq Stranded mRNA and TruSeq Stranded Total RNA Library Prep Kits. Version 2 contains improvements for 8 of the 192 index oligos in plate 20022371, with no changes to the remaining 184. Purchase library preps and probe panels separately.

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IDT for Illumina – TruSeq DNA UD Indexes v2 (96 Indexes, 96 Samples)

20040870

Includes 96, 8 bp indexes sufficient for labeling 96 samples and is compatible with TruSeq Nano and TruSeq PCR-Free Library Prep Kits. Version 2 contains improvements for 8 of the 192 index oligos in plate 20022370, with no changes to the remaining 184. Purchase library preps and probe panels separately.

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FAQs

The Illumina Adapter Sequences Document lists index adapter sequences and all other adapter sequences.

Yes. Anchor plates are required for RNA library prep kits and are already included in Illumina RNA UD Indexes Sets A-D and IDT for Illumina RNA UD Indexes Sets A-D.

The level of index hopping will not change with Illumina DNA/RNA UD Indexes, but the index hopped reads can be removed bioinformatically from the demultiplexed data.

Unique dual indexing adds completely unique, unrelated index sequences to both ends of each fragment of DNA during library preparation. This allows large numbers of libraries to be pooled and sequenced simultaneously during a single run. Compared to other indexing methods, unique dual indexing mitigates index hopping by filtering hopped reads.

/ Results

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