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
- NEW V2 Indexing Primers—no longer requires separate uracil-tolerant polymerase, and supports conversion of a wider range of libraries
- Industry-leading provider of high-purity ligation-based and PCR-indexing solutions for NGS
- Our xGen solutions for Ultima allow researchers to take advantage of Ultima Genomics' cutting-edge advancements in sequencing throughput and economy, by enabling conversion of a variety of 3rd party sequencing libraries, and supporting PCR-free WGS workflows
- Barcodes are designed with edit distance in mind to minimize any sequence errors from PCR or sequencing that might impact demultiplexing
- 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† | |||
|---|---|---|---|---|---|
| IDT xGen Library Prep Kits | 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 | ✓ | ||||
| Third-party library conversion†† | ✓ | ||||
* 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
†† See additional details below on library designs are supported
Convert a variety of existing 3rd party libraries, for running on a UG 100 Sequencer
New xGen Indexing Primers V2 allow for more third-party library designs to be converted for running on an Ultima sequencer, without the need to source an uracil-tolerant amplification module separately.
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
Below is a cross reference from the Ultima Catalog number to the IDT Catalog number with library type compatibility. Please contact us with any questions.
| Product | IDT catalog number | Replaces Ultima Catalog # | Third-party library compatibility** |
|---|---|---|---|
| xGen™ UG-tR2 Universal Primer for Ultima, 96 rxn* | 10028399 | UG0111 |
|
| xGen™ UG Universal R Primer for Ultima, 96 rxn* | 10028400 | UG0110 |
|
| xGen™ UG-srR2 Universal Primer for Ultima, 96 rxn* | 10028411 | UG0112 |
|
* Indexing primers are also required for the library conversion workflow
** Subject to change. You can find the latest version of Ultima Genomics’ 3rd Party Library Conversion protocol hosted here.
PCR-free whole genome sequencing (WGS) workflow
Direct sequencing is for applications with adequate gDNA input to support a PCR-free workflow or when indexing by ligation is preferred.
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 v2 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,
|
10 µM (each primer) |
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 | 96 reactions per plate/tube | 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.
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.
How will my xGen™ UG-tR1 Indexing Primers for Ultima be delivered?
How will my xGen™ PCR-Free Adapters for Ultima or xGen™ HybCap Adapters for Ultima be delivered?
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 shelf life and recommended storage conditions for the xGen™ HybCap Library Amp Primer Mix for Ultima?
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.
Which sequencing platform should be used for the xGen™ Adapters or Indexing Primers for Ultima?
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.
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.