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xGen for DNBSEQ

xGen™ for DNBSEQ™

Trusted IDT xGen NGS chemistries for emerging sequencers

Whether your project requires a basic indexing solution, or a more sophisticated design for higher accuracy, we have the products and expertise to deliver the right solution for DNBSEQ platforms.

xGen NGS—made platform-agnostic

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IDT has several solutions available for customers sequencing on a DNBSEQ™ platform. Our products support both WGS and targeted (hybridization capture) sequencing workflows.

  • IDT is the leading provider for high-purity PCR-indexing solutions for NGS—now proudly offering adapters for sequencing on a DNBSEQ™ system!
  • Barcodes designed with edit distance in mind, to minimize any sequence errors from PCR or sequencing that might impact demultiplexing
  • IDT is the first to offer stocked Universal Blocking Oligos for the DNBSEQ™ system, designed specifically for the native adapters

Product details

Table 1. xGen for DNBSEQ library prep compatibility table


xGen™ Stubby Adapter-UDI Primers for DNBSEQ™
xGen Broad-Range RNA Library Prep Kit 
xGen RNA Library Prep Kit 
 
xGen DNA Library Prep (MC or EZ) Kit✓*
xGen DNA Library Prep (MC or EZ) UNI Kit✓
 
xGen ssDNA & Low-Input DNA Library Prep Kit 
 
xGen Methyl-Seq Library Prep Kit 
 
xGen cfDNA & FFPE DNA Library Prep Kit 

* Can be used if the stubby adapter included in the library prep kit is swapped out for the xGen Stubby Adapter for DNBSEQ

Use the xGen™ Stub Adapter-UDI Primers DNBSEQ™ products to perform indexing PCR on NGS libraries that require TA-ligation (using the included stubby adapter) for DNBSEQ-compatible library construction workflows that support indexing by PCR. Note, when using an IDT Library Prep Kit, the xGen™ Stubby Adapter DNBSEQ™ should be used instead of the adapter supplied in the IDT Library Prep Kit. For other commercial library prep workflows, refer to your library prep kit protocol for further instructions prior to using these products.

xGen™ Stub Adapter-UDI Primers DNBSEQ™ are available in two reaction sizes (16 and two sets of 96). xGen™ Stubby Adapter DNBSEQ™ is loaded in a multi-use tube and the xGen™ UDI Primers DNBSEQ™ are loaded into single-use plates.

  • Single-use plates: The indexing primers are loaded into single-use 96-well plates containing a pierceable seal. The unique dual index (UDI) has a barcode length of 10 nucleotides. Each well contains one index pair for indexing one sample.
  • xGen™ Stub Adapter-UDI Primers DNBSEQ™, 16 rxn
  • xGen™ Stub Adapter-UDI Primers DNBSEQ™ P1, 96 rxn
  • xGen™ Stub Adapter-UDI Primers DNBSEQ™ P2, 96 rxn

Sample multiplexing:

  • For an 8-plex use any column
  • For an (8 + N)-plex use any column + any N random wells in other columns

If you have specific questions, contact us.

xGen™ products for DNBSEQ™ offers several benefits:

  • IDT is the leading provider of NGS indexing products, so you can be confident in the quality of your xGen™ Stub Adapter-UDI Primers DNBSEQ™
  • IDT is first to offer a stocked universal blocking oligo designed specifically for DNBSEQ™ libraries
  • Prevent adapter cross-hybridization—Adapter sequences are ligated to all library fragments, both on-target and off-target before enrichment. These adapter sequences can hybridize with each other during enrichment, creating a "daisy-chain" effect; off-target fragments are captured alongside on-target fragments which can impact sequencing efficiency. The xGen™ Universal Blocking Oligos for DNBSEQ™ bind to the native DNBSEQ™ adapters and help prevent adapter cross-hybridization
  • Universal blocking oligos reduce workflow steps by not requiring barcode-specific strand blocking; removes workflow steps that help reduce error; require less materials to store
  • xGen™ Library Amplification Primer Mix for DNBSEQ™ receives functional testing that ensures high performance library amplification post-capture PCR

Table 2. Product specifications 

Indexing optionxGen Stubby Adapter-UDI Primers for DNBSEQ
Sample index length10 nucleotide indexes
Concentration

15 µM (stubby adapter),
10 µM (each primer)

Shipping containerTube (stubby adapter),
Single use plates (primers)
Reactions1 reaction per primer pair
Platform compatibilityAny DNBSEQ™ instrument

Product data

Methyl-seq library preparation workflow comparisons

The xGen Methyl-Seq DNA Library Prep Kit has a post-bisulfite library preparation workflow to maximize library complexity by converting bisulfite-induced single-stranded fragments directly into library molecules. Traditional methods construct libraries from dsDNA using methylated adapters followed by bisulfite conversion that leads to significant library loss due to bisulfite-induced DNA fragmentation. The random priming methods are also post-bisulfite but have reduced library complexity due to a lower efficiency biased workflow (see Table 2; Figure 3).

Frequently asked questions

No, these two stubby adapters are not cross-compatible—they are platform-specific.

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xGen Library Amp Primer Mix for DNBSEQ can be used for amplification of libraries made from the xGen Stubby Adapter-UDI Primers for DNBSEQ.

The xGen Library Amp Primer Mix for DNBSEQ is used for PCR amplification during the hybridization capture enrichment workflow. Subsequent library circularization must be done using the MGIEasy Circularization Kit available from MGI, (MGI item number 1000005259) found here, prior to sequencing on a DNBSEQ platform.

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No. Only xGen Universal Blockers for DNBSEQ should be used for hybridization capture of libraries prepared using the xGen Stubby Adapter-UDI Primers for DNBSEQ.

Other xGen Blocking Oligos available from IDT are not compatible with DNBSEQ libraries.

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xGen Stubby Adapter for DNBSEQ is delivered in a multi-use tube at 15 µM.

xGen UDI Primers for DNBSEQ are delivered premixed at 10 µM each in a single-use plate and sealed with a pierceable seal. Each well contains a specific unique dual index (UDI) for indexing one sample.

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Index sequences are available in the ‘Resources’ section on the product page . For further questions on the adapter sequences, we recommend contacting MGI at us-techsupport@completegenomics.com.

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We recommend storing the xGen Library Amp Primer Mix for DNBSEQ at –20°C. The date of manufacture is included on the product label and its corresponding Certificate of Analysis, which can be found by searching by batch/lot number on the product label. We also recommend using the products within 1 year of the date of manufacture.

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We recommend storing the xGen Universal Blockers for DNBSEQ at –20°C. The date of manufacture is included on the product label and its corresponding Certificate of Analysis, which can be found by searching by batch/lot number on the product label. We also recommend using the products within 1 year of the date of manufacture

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We recommend storing the xGen Stubby Adapter-UDI Primers for DNBSEQ at –20°C. The date of manufacture is included on the product label and its corresponding Certificate of Analysis, which can be found by searching by batch/lot number on the product label. We also recommend using the products within 1 year of the date of manufacture.

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No, this is not recommended.

All our plate-based indexing products contain overage to allow for pipetting error, so we recommend pipetting directly out of the index plate and into a separate reaction plate or tube.

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The xGen Stubby Adapter-UDI Primers for DNBSEQ libraries are compatible with an MGI DNBSEQ sequencer.

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This can vary by library preparation method; consult the specific protocol you are using for the exact input range.

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We recommend using a buffer made of 10 mM Tris, 0.1 mM EDTA, and 100 mM NaCl, pH 8.0 (such as the IDT NGS Adapter Buffer, Cat. No. 10006743) to dilute the xGen Stubby Adapter for DNBSEQ. Keeping the adapters duplexed requires a buffer with a high salt concentration.

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No, neither the xGen Stubby Adapters nor UDI Primers for DNBSEQ are methylated.

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No, neither the xGen Stubby Adapter-UDI Primers for DNBSEQ nor xGen UDI primers for DNBSEQ contain UMIs.

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You should use an adhesive plate seal over the punctured but unused wells to prevent future cross‑contamination. Do not heat‑seal the plate twice.

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All related FAQs

References

  1. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012 May 29;13(7):484-92. doi: 10.1038/nrg3230. PMID: 22641018.
  2. Luo C, Keown CL, Kurihara L, et al. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science (New York, NY). 2017;357(6351):600-604.
  3. Luo C, Rivkin A, Zhou J, et al. Robust single-cell DNA methylome profiling with snmC-seq2. Nat Commun. 2018;9(1):3824.
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