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xGen™ for Element Biosciences

Trusted IDT xGen NGS chemistries for emerging sequencers

Are you working on Element Biosciences platforms? IDT has solutions such as adapters, universal blockers, and library amplification primer mixes that are designed specifically for sequencing on any Element AVITI™ System.

xGen NGS—made platform-agnostic

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IDT has several solutions available for customers sequencing on the Element AVITI System. These products support both WGS and targeted (hybridization capture) sequencing workflows.

  • IDT is the leading provider for high-purity PCR-indexing solutions for NGS—and we are now proud to offer adapters for sequencing on the Element AVITI 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 Element system, designed specifically for their native adapters

Product details

Table 1. xGen for Element Biosciences library prep compatibility table.


xGen Stubby Adapter-UDI Primers for Element
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 Element

Use xGen Stubby Adapter-UDI Primers for Element products to perform indexing PCR on NGS libraries that require TA-ligation (using the included stubby adapter) for Element Biosciences-compatible library construction workflows that support indexing by PCR. Note, when using an IDT library prep kit, the xGen Stubby Adapter for Element 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 Stubby Adapter-UDI Primers for Element are available in two reaction sizes (16 and 96). xGen Stubby Adapter for Element is loaded in a multi-use tube and the xGen UDI Primers for Element are loaded into single-use, 96-well plates containing a pierceable seal. The unique dual index (UDI) has a barcode length of 9 nucleotides. Each well contains one specific index pair for indexing one sample. The xGen Universal Blockers for Element and xGen Library Amplification Primer Mix for Element are both delivered in multi-use tubes.

Sample multiplexing:

  • For a 4-plex pool, use wells A1–D1
  • For a 8-plex pool, use any column except column 6
  • For a 12-plex pool, use any row
  • For a 16-plex pool, use columns 1 and 2
  • For a 24-plex pool, use columns 1, 2, and 3

If you have specific questions, please contact us.

xGen products for Element Biosciences offer several benefits:

  1. IDT is a leading provider of NGS indexing products, so you can be confident in the quality of your xGen Stubby Adapter-UDI Primers for Element.
  2. IDT is first to offer a stocked universal blocking oligo designed specifically for Element Biosciences libraries.
  3. 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, with off-target fragments being captured alongside on-target fragments, which can impact sequencing efficiency. xGen Universal Blocking Oligos for Element bind to the Element-specific adapter sequences on a designated strand to help prevent adapter cross-hybridization.
  4. Universal blocking oligos reduce workflow steps by not requiring barcode-specific strand blocking; removing workflow steps help reduce error; less materials to store.
  5. xGen Library Amplification Primer Mix for Element receives functional testing to ensure high performance library amplification in post-capture PCR.

Table 2. Product specifications.

Indexing optionxGen Stubby Adapter-UDI Primers for Element
Sample index length9 nucleotide indexes
Concentration

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

Shipping containerTube (stubby adapter),
Single-use plates (primers)
Reactions1 reaction per adapter
Platform compatibilityElement AVITI

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 Element can be used for amplification of libraries made from the xGen Stubby Adapter-UDI Primers for Element and is not compatible with other sequencing platforms. The xGen Library Amp Primer Mix for Element is used for PCR amplification during the hybridization capture enrichment workflow.

For customers not using an AVITI™ Cloudbreak system*, subsequent library circularization must be performed using the Elevate™ Library Circularization Kit (Element Biosciences catalog # 830-00001) prior to sequencing on the Element Biosciences platform.

* Off‑sequencer circularization is not required for libraries run on an AVITI Cloudbreak system.

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No. Only xGen Universal Blockers for Element should be used for hybridization capture of libraries prepared using xGen Stubby Adapter‑UDI Primers for Element. Other xGen blocking oligos available from IDT are not compatible with Element‑specific libraries.

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

xGen UDI Primers for Element 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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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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Sequences for the xGen™ Stubby Adapter‑UDI Primers for Element can be obtained from our Applications Support team. Index sequences are available in the 'Resources' section.*

* Sequences are provided under license to IDT by Element Biosciences and may be subject to terms and conditions. Not for commercial resale.

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Store the xGen Library Amp Primer Mix for Element at –20°C. The date of manufacture is included on the product label and its corresponding Certificate of Analysis (CoA), which can be found by searching by batch/lot number on the product label. IDT recommends using the products within 1 year of the date of manufacture.

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Store the xGen Universal Blockers for Element at –20°C. The date of manufacture is included on the product label and its corresponding Certificate of Analysis (CoA), which can be found by searching by batch/lot number on the product label. IDT recommends using the products within 1 year of the date of manufacture.

View FAQ

Store xGen Stubby Adapter‑UDI Primers for Element at –20°C.

The date of manufacture is included on the product label and its corresponding Certificate of Analysis (CoA), which can be found by searching by batch/lot number on the product label. IDT recommends using the products within 1 year of the date of manufacture.

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The xGen Stubby Adapter‑UDI Primers for Element generate Element‑compatible NGS libraries and should be sequenced on an Element Biosciences instrument.

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The amount can vary depending on the library prep workflow. We recommend checking your specific protocol 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, catalog # 10006743) to dilute the xGen Stubby Adapter for Element.

Keeping the adapters duplexed requires a buffer with a high salt concentration.

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No, neither the xGen Stubby Adapter nor UDI Primers for Element are methylated.

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No, neither the xGen Stubby Adapter nor UDI primers for Element contain UMIs.

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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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