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1000000041074 v17
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July 2026
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Corrected two-plex through eight-plex pooling strategies for NovaSeq X Series or NextSeq 1000/2000 with XLEAP-SBS chemistry on Illumina UD Indexes Set A and Set B. |
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Corrected nine-plex pooling strategies for Illumina UD Index Set A and Set B, and their example figures. |
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Corrected two-plex through eight-plex pooling strategies for NovaSeq X Series or NextSeq 1000/2000 with XLEAP-SBS chemistry on TruSeq UD Indexes. |
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Redesigned colored layout examples. |
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1000000041074 v16
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December 2025
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Clarified current XLEAP-SBS chemistry recommendations are only applicable to NovaSeq X Series and NextSeq 1000/2000 instruments. |
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Added MiSeq i100 Series chemistry clarifications. |
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Added 2 plex information for Illumina Single Cell Prep UDI Mix Strip and Unique Dual Indexes. |
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Corrected index B09 of Ampliseq CD Indexes for Illumina Set C. |
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Corrected index B09 of IDT for Illumina UD Indexes Set C. |
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Removed references to HiSeq Systems and IEM. |
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1000000041074 v15
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March 2025
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Added Illumina Single Cell RNA Indexes.
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1000000041074 v14
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January 2025
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Clarified pooling strategies for instruments using XLEAP-SBS chemistry. |
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Added MiSeq i100 Series information. |
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1000000041074 v13
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February 2024
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Added NextSeq 1000/2000 XLEAP-SBS chemistry information.
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1000000041074 v12
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September 2023
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Added NovaSeq X Series information. |
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Added plate layout and pooling strategies for Illumina UD Indexes, Set A-D. |
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Added clarification for V2 indexes used with IDT for Illumina UD Indexes Set C and Set D. |
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Reorganized the following content to improve continuity and navigation: |
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Color balance and index adapter combinations |
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IDT for Illumina TruSeq UD Indexes |
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1000000041074 v11
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April 2021
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Corrected Plexity 6 [Option 1] details in pooling strategy tables for IDT for Illumina UD Indexes and Nextera DNA CD Indexes (96 Indexes, 96 Samples). |
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1000000041074 v10
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July
2020
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Replaced UDI0015, UDI0016, UDI0055, UDI0056, UDP0252, UDP0258, UDP0289, UDP0290, UDP0291, and UDP0301 with V2 versions. |
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Added IDT for Illumina-PCR UD Indexes Set 1, 2, 3, 4. |
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1000000041074 v09
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March 2020
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Generalized references to NextSeq Systems to include all versions. |
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Added NextSeq 2000 information to Two-Channel Chemistry section. |
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Added Instrument Run Setup to Color Balance section. |
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1000000041074 v08
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October 2019
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Corrected the third option for TruSeq RNA Single Indexes Set B four-plex pooling strategy. |
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Added index plate layouts for IDT for Illumina TruSeq–UD Indexes (24 Indexes, 96 Samples). |
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1000000041074 v07
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May 2019
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Added index plate layouts for IDT for Illumina Nextera DNA UD Indexes Sets B–D. |
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Identified the IDT for Illumina Nextera DNA UD index plate layout as IDT for Illumina Nextera DNA UD Indexes Sets A. |
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Updated section on TruSeq Small RNA indexes to improve clarity and accuracy. |
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1000000041074 v06
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February 2019
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Added index plate layouts for AmpliSeq CD Indexes Sets B–D for Illumina. |
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Identified the AmpliSeq for Illumina index plate layout as AmpliSeq CD Indexes Set A for Illumina. |
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1000000041074 v05
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December 2018
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Corrected the Index 1 (i7) index adapter in well C2 of the AmpliSeq CD Indexes for Illumina plate to Q7008.
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1000000041074 v04
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November 2018
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Combined, renamed, and reorganized all sections to improve continuity, facilitate navigation, and eliminate redundancy. |
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Consolidated graphics depicting pooling strategies for IDT for Illumina Nextera DNA UD Indexes and Nextera DNA CD Indexes (96 Indexes, 96 Samples). |
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Added pooling guidelines for Nextera XT Index Kit v2 and Nextera Index Kit. |
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Added information on Illumina Experiment Manager, Local Run Manager, and BaseSpace Sequence Hub. |
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Added good and bad examples of color balance on a four-channel system. |
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Identified all Index 1 (i7) and all Index 2 (i5) adapters for Nextera DNA CD Indexes (24 Indexes, 24 Samples). |
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Updated plate layouts to remove duplicate index adapter names and show the Index 1 (i7) adapters first. |
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Updated descriptions of one-, two-, and four-dye chemistry. |
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1000000041074 v04 continued
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November 2018
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Described dual indexing options: combinatorial dual (CD) and unique dual (UD) indexes. |
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Described pooling strategies for TruSeq CD Indexes and updated style of the graphics (the strategies have not changed). |
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Referenced Indexed Sequencing Overview (document # 15057455) for indexing workflows on Illumina sequencing systems. |
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Clarified the following points: |
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TruSeq CD Indexes replaced TruSeq HT Indexes. |
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For two-plex, dual-indexing with TruSeq CD Indexes, pool diagonally. |
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Single-indexing with TruSeq CD Indexes requires dual index adapters. |
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Removed the following sequences, which are available in Illumina Adapter Sequences (document # 1000000002694): |
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Index adapter sequences for Nextera DNA CD Indexes (for Nextera DNA Flex). |
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Index adapter and adapter trimming sequences for AmpliSeq for Illumina. |
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Corrected column-based, three-plex pooling strategy for AmpliSeq for Illumina. |
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Corrected names of the following items: |
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Index adapters UDP0001–UDP0009 to include four digits. |
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1000000041074 v03
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October 2018
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Added information on IDT for Illumina Nextera DNA UD Indexes. |
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Consolidated low-plexity guidelines. |
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Corrected tables for Nextera DNA Flex 96 CD Indexes. |
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Removed single indexing information for IDT for Illumina TruSeq DNA UD Indexes, which is compatible with dual indexing only. |
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Removed incorrect guidelines for: |
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Low plexity sequencing on the NovaSeq 6000 System. |
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Low throughput for Nextera DNA Flex combinatorial dual indexes. |
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1000000041074 v02
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May 2018
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Added information on one-channel sequencing for the iSeq 100 System.
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1000000041074 v01
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January 2018
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Added pooling guidelines for AmpliSeq for Illumina and Nextera DNA Flex libraries.
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1000000041074 v00
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October 2017
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Initial release.
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