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).
Illumina UD Indexes enable sequencing of significantly more samples per run without compromising data quality.
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.
| Instruments | MiSeq System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiSeqDx in Research Mode, MiniSeq System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000Dx in Research Mode, NextSeq 500 System, NovaSeq 6000 System, NovaSeq X Plus System |
|---|---|
| Mechanism of action |
Ligation-based adapters: IDT for Illumina TruSeq RNA and DNA UD Indexes v2; PCR-based adapters: Illumina DNA/RNA UD Indexes Set A-D and IDT for Illumina DNA/RNA UD Indexes Set A-D; Ligation and PCR-based adapters: Illumina RNA UD Indexes Set A-D and IDT for Illumina RNA UD Indexes Set A-D |
| Multiplexing |
Illumina UD Indexes and IDT for Illumina UD Indexes: Up to 384-plex. IDT for Illumina TruSeq Indexes: Up to 96-plex. |
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 DNA/RNA UD Indexes Set A-D and IDT for Illumina DNA/RNA UD Indexes Set A-D
IDT for Illumina TruSeq RNA UD Indexes v2
IDT for Illumina TruSeq DNA UD Indexes v2
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.
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.
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.
List Price:
Discounts:
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.
List Price:
Discounts:
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.
List Price:
Discounts:
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.
List Price:
Discounts:
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.
List Price:
Discounts:
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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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.
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