Processing
xGen™ for Ultima Genomics®
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 Ultima Genomics platforms.
xGen NGS—made platform-agnostic
Ordering
- IDT is a leading provider of high-purity ligation-based and PCR-indexing solutions for NGS, and now we are proud to offer adapters and indexing primers for sequencing on Ultima Genomics systems
- xGen for Ultima products are available to support both whole genome sequencing (WGS) and targeted sequencing (via hybridization capture) workflows
- Barcodes are 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 Ultima system—designed specifically for their native adapters
Product details
IDT has several solutions available for customers sequencing on an Ultima Genomics platform—the best solution for you depends on your workflow. Please refer to Table 1 for adapter and indexing primer recommendations based on library prep method and the WGS/target enrichment workflow information tabs for guidance specific to your whole genome sequencing or hybridization capture workflow needs.
Table 1. Recommended xGen for Ultima adapters and indexing primers based on compatibility with library prep methods.
| PCR-Free Adapters | HybCap Adapters* | Indexing Primers† | ||
|---|---|---|---|---|
| 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 | ✓ | |||
* Only the HybCap adapters may be used for construction of libraries intended for hybridization capture target enrichment
† Amplification must be done using a uracil-tolerant polymerase. IDT recommends the UG Amplification kit (catalog
# 20020007), available from Ultima Genomics
Whole genome sequencing (WGS) workflow
We offer xGen for Ultima solutions for both PCR-free and PCR-dependent WGS workflows, each with flexible options depending on the number of samples.
- xGen PCR-Free Adapters for Ultima Genomics
- For applications with adequate gDNA input to support a PCR-free workflow, or when indexing by ligation is preferred
- xGen Indexing Primers for Ultima Genomics
- For applications where indexing by PCR is preferred
- Requires uracil-tolerant PCR mix, found in the UG Amplification Kit available from Ultima Genomics (catalog # 20020007)
- xGen Stubby Adapter (catalog # 10005974 or 10005924, sold separately) may be required; refer to Table 1 and Figure 1 for details
All xGen sample indexing products for Ultima are loaded into single-use 96-well plates containing a pierceable seal. The sample barcode has a length of either 15 or 17 nucleotides—consult the index list and plate map for further details. Each well contains material for indexing one sample.
Sample multiplexing:
- For an 8-plex, use any column
Please contact us with any questions.
Figure 1. xGen for Ultima Genomics WGS workflow
Target enrichment workflow
Confidently perform target enrichment via hybridization capture with the following xGen for Ultima HybCap products:
- xGen HybCap Adapters for Ultima Genomics
- Used for library construction prior to hybridization capture
- Requires conditioning with the Ultima Genomics UG Library Amplification Kit prior to sequencing*
- xGen HybCap Lib Amp Primers for Ultima Genomics
- Designed to increase yield for sequencing post-hybridization capture
- xGen Universal Blockers for Ultima Genomics
- Reduces non-specific adapter interaction during hybridization
* Different adapters are required for hybridization capture due to the modifications found on the native Ultima adapters. Due to this, after hybridization capture, conditioning of the final library using the UG Amplification Kit available from Ultima Genomics (catalog # 20020007) is required prior to sequencing on the Ultima platform.
All xGen sample indexing products for Ultima are loaded into single-use 96-well plates containing a pierceable seal. The sample barcode has a length of either 15 or 17 nucleotides—consult the index list and plate map for further details. Note that there is no difference in the index sequences between products used for WGS or target enrichment. Each well contains material for indexing one sample. The xGen Universal Blockers and HybCap Lib Amp Primers for Ultima are both delivered in multi-use tubes.
Sample multiplexing:
- For an 8-plex, use any column
Please contact us with any questions.
Figure 2. xGen™ for Ultima Genomics® Targeted (Hybridization Capture) Sequencing Workflow.
Table 2. Product specifications
| Indexing option | xGen PCR-Free Adapters for Ultima Genomics | xGen Indexing Primers for Ultima Genomics | xGen HybCap Adapters for Ultima Genomics |
|---|---|---|---|
| Sample index length | 15 or 17 nucleotide indexes | 15 or 17 nucleotide indexes | 15 or 17 nucleotide indexes |
| Concentration | 15 µM total, | 20 µM total, | 15 µM total, |
| Shipping container | 96-well plates, single use | 96-well plates, single use | 96-well plates, single use |
| Reactions | 1 reaction per adapter | 1 reaction per primer pair | 1 reaction per adapter |
| Platform compatibility | UG 100™ | UG 100 | UG 100 |
Resources
Frequently asked questions
What methods are recommended to quantify my libraries prepared using xGen™ PCR-Free Adapters for Ultima?
Libraries prepared using xGen PCR-Free Adapters for Ultima must be quantified prior to sequencing by qPCR using library quantification primers and standards available from Ultima (UG Library Quantification Kit, Ultima part number L09) and a 2X SYBR® qPCR master mix which must be purchased separately.
Quantification using fluorometric or electrophoretic methods are not suitable for quantifying libraries prepared using xGen PCR-Free Adapters for Ultima.
What plate sealing guidelines should I follow when fewer than 16 or 96 libraries are prepared?
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.
How will my xGen™ PCR-Free Adapters for Ultima or xGen™ HybCap Adapters for Ultima be delivered?
How will my xGen™ Indexing Primers for Ultima be delivered?
Can universal or standard blocking oligos be used with libraries made from the xGen™ Adapters and Indexing Primers for Ultima?
No. Only xGen™ Universal Blockers for Ultima should be used for hybridization capture of libraries prepared using the xGen™ Adapters and Indexing Primers for Ultima. Other xGen™ blocking oligos available from IDT are not compatible with Ultima libraries.
What buffer should I use to dilute the xGen™ Stubby Adapter, xGen™ PCR-Free Adapters for Ultima, and xGen™ HybCap Adapters for Ultima?
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, xGen™ PCR-Free Adapters for Ultima, and xGen™ HybCap Adapters for Ultima.
Keeping the adapters duplexed requires a buffer with a high salt concentration.
What amount of xGen™ Adapters or Indexing Primers for Ultima should I use for library prep?
This can vary by library prep method; consult the specific protocol you are using for the exact input range.
Which sequencing platform should be used for the xGen™ Adapters or Indexing Primers for Ultima?
The xGen™ Adapters and Indexing Primers for Ultima generate Ultima Genomics compatible libraries and should be sequenced on an Ultima Genomics instrument.
Can adapter ligation be carried out in the provided 96-well plate of xGen™ PCR-Free Adapters for Ultima, or xGen™ HybCap Adapters for Ultima?
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.
What is the shelf life and recommended storage conditions for the xGen™ Adapters or Indexing Primers for Ultima?
Store all xGen™ Adapters or Indexing Primers for Ultima 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. IDT recommends using the products within 1 year of the date of manufacture.
What is the shelf life and recommended storage conditions for the xGen™ Universal Blockers for Ultima?
Store the xGen™ Universal Blockers for Ultima 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. IDT recommends using the products within 1 year of the date of manufacture.
What is the shelf life and recommended storage conditions for the xGen™ HybCap Library Amp Primer Mix for Ultima?
Store the xGen™ HybCap Library Amp Primer Mix for Ultima 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. IDT recommends using the products within 1 year of the date of manufacture.
What are the sequences for the xGen™ Adapters and Indexing Primers for Ultima?
Sequences of the xGen™ Adapters and Indexing Primers for Ultima are proprietary. Index sequences are available in the resources section.
What is the difference between xGen™ HybCap Lib Amp Primer Mix for Ultima and other library amplification mixes, such as xGen™ Library Amplification Primer Mix?
The xGen™ HybCap Lib Amp Primer Mix for Ultima is used for on-bead PCR amplification during the enrichment workflow. Subsequent library conditioning must be done using library amplification primers available from Ultima Genomics, PN 20020007 found at https://www.ultimagenomics.com/ prior to sequencing on the Ultima platform.
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