For a list of compatible index kits, see Compatible Products.
The Nextera XT kit is recommended for small genomes, PCR amplicons greater than 300 bp, plasmids, microbial genomes, concatenated amplicons, and double-stranded cDNA.
The different index kit versions (v1 and v2) are not chemically different. The v2 kits were introduced to provide more index combinations. When Sets A–D are combined, up to 384 unique index combinations are possible. If you plan to multiplex more than 96 samples, the v2 index kits are recommended.
The v1 and v2 index kits provide some of the same indexes. For information about which indexes are included with each kit, see the Illumina Adapter Sequences Document.
Yes, this kit is compatible with IDT for Illumina Nextera DNA UD Indexes. However, the indexes are not compatible with bead-based normalization. Use the standard or manual normalization workflow with IDT for Illumina Nextera DNA UD Indexes. For more information, see Best Practices for Standard and Bead-Based Normalization in Nextera XT DNA Library Preparation Kits.
The estimated time to prepare eight samples is ~90 minutes for the prep and 70 minutes for bead-based normalization (BBN). The estimated time for 96 samples is ~3 hours for the prep and 90 minutes for BBN.
Use the Nextera XT DNA kit for microbial genomes < 5 Mb. For larger genomes, use the Nextera DNA, TruSeq DNA PCR-Free, or TruSeq Nano DNA kits.
Smaller amplicon inputs into Nextera XT preps typically yield smaller insert size ranges. To maximize recovery of smaller fragments out of the AMPureXP cleanup we recommend > 300 bp to ensure even coverage across the length of the DNA fragment. An expected drop off in sequencing coverage about 50 bp from each distal end of a fragment may be seen. This is because the tagmentation reaction cannot add an adapter right at the distal end of a fragment. For PCR amplicon sequencing this can be easily averted by simply designing your amplicons to be ~100 bases larger than the desired insert to be sequenced.
For amplicons greater than 500 bp, Illumina recommends using a 0.6x AMPure XP cleanup (30 μl bead volume). For amplicons less than 500 bp, Illumina recommends using a 1.8x AMPure XP cleanup (90 μl bead volume) to maximize yield.
To obtain higher quality sequencing data, Illumina recommends sequencing samples with high diversity and avoiding monotemplate stretches during sequencing. Low diversity can occur with pools of one or a few amplicons. Additionally, it is important to maintain color balance for each base of the read or index read being sequenced, otherwise sequencing could fail due to registration failure. See the MiSeq System User Guide for Local Run Manager (document # 15027617) or the MiSeq System User Guide for MiSeq Reporter (document # 1000000061014) for recommendations on low diversity libraries. For information on low plexity pooling guidelines, see the Illumina Adapters Pooling Guide (document # 1000000041074).
For recommended index combinations, see Nextera Low Plex Pooling Guidelines (Pub. No. 770-2011-044).
Library normalization is the process of obtaining equal amounts of library before loading the libraries onto the flow cell. The Nextera XT DNA kit includes reagents for bead-based normalization.
Use the following guidelines to determine which normalization method to perform: standard or bead-based. For more information, see Best Practices for Standard and Bead-Based Normalization in Nextera XT DNA Library Preparation Kits (Pub. No. 470-2016-007).
When creating a sample sheet in Illumina Experiment Manager (IEM), the software alerts you when improper combinations are used. Thus, creating your sample sheet before beginning library prep and pooling is highly recommended.
Excepting HiSeq 2500, IEM does not provide notification for color balance problems. For guidance, see the Index Adapters Pooling Guide.
Always pool samples with valid index combinations to avoid image registration failures. MyIllumina.com provides bulletins on library pooling, including pooling guidelines for the NextSeq and MiniSeq systems.
Completing Nextera XT DNA library prep requires ordering the library prep kit and corresponding index kits: Nextera XT DNA Library Prep Kits (catalog # FC-131-1024, FC-131-1096) and corresponding Nextera XT Index Kits (catalog # FC-131-1001, FC-131-2001, FC-131-2003, FC-131-2004) or IDT for Illumina Nextera DNA UD Indexes (catalog # 20027213). Nextera XT Index Kits are optimized for the Nextera XT DNA Library Prep Kits and are not interchangeable with the Nextera DNA Library Prep Kit. The index plate fixture (catalog # FC-130-1005) is not included in the library prep kits or index kits, and must also be purchased separately.
The Nextera XT protocol is optimized for 1 ng of input DNA total. Illumina strongly recommends quantifying the starting genomic material. Nextera XT library prep kits use an enzymatic DNA fragmentation step and thus can be more sensitive to DNA input compared to mechanical fragmentation methods. The ultimate success of the assay strongly depends on using an accurately quantified amount of input DNA library. Therefore, the correct quantitation of the DNA library is essential.
To obtain an accurate quantification of the DNA library, quantify the starting DNA library using a fluorometric-based method specific for duplex DNA, such as the Qubit dsDNA BR Assay system. Use 2 μl of each DNA sample with 198 μl of the Qubit working solution for sample quantification. Avoid methods that measure total nucleic acid content (e.g., nanodrop or other UV absorbance methods) because common contaminants such as ssDNA, RNA, and oligos are not substrates for the Nextera XT assay.
Although most amplicons of interest are not likely to be high GC-content, coverage of high GC-content amplicons might have more variability compared to other amplicons.
A TruSeq Dual Index Sequencing Primer Box PE (PE-121-1003) or TruSeq Dual Index Sequencing Primer Box SR (FC-121-1003) is needed to sequence Nextera XT libraries on a HiSeq 2500 using TruSeq v3 chemistry. Use the PE box with paired-end flow cells and the SR box with single-read flow cells.
Other HiSeq 2500 chemistry and other systems do not require this additional box.
Most sequencing systems require 2–4 nM denatured library. For instructions, see the denature and dilute instructions for your instrument.
For paired-end flow cells, dual indexing now requires 23 additional cycles of sequencing - eight cycles for the Index 1 (i7) Read, eight cycles for the Index 2 (i5) Read, plus seven non-imaging, chemistry-only cycles at the beginning of the Index 2 (i5) Read. For single-read flow cells, dual indexing only requires 16 additional cycles of sequencing - eight cycles for the Index 1 (i7) Read and eight cycles for the Index 2 (i5) Read.