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