IDT Next Generation Sequencing adapterek és indexek
Adapters & indexing primers are a key component of NGS library preparation workflow. 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.
xGen NGS—made to differentiate.
FIGYELEM!
IDT termékek szállítási költségei 2024-től:
A szintézis helyétől, valamint a szállítási körülményektől függően az alábbi költségek kerülnek felszámításra:
-
Belgiumból: nettó 6 900 Ft
USA-ból: nettó 34 000 Ft
Belgiumból, szárazjégen: nettó 37 000 Ft
USA-ból, szárazjégen: nettó 45 000 Ft
- Oldatok szállítási költsége: mennyiség és súly függvénye, kérjen ajánlatot a Bio-Science Kft.-től!
Általános tájékoztató az IDT USA gyártási központjából érkező „custom” termékcsoportokról:
szintetikus biológiai termékek:
- Gének
- gBlocks, eBlocks
- Ultramerek
- RNS-oligók
- CRISPR guide RNS-ek
- oPools
qPCR próbák:
a szintézis helye a szekvencia komplexitásától, valamint a választott festék/ quencher kombinációtól függ
szolgáltatások:
- PAGE tisztított termékek
stock termékek:
nem áll teljes lista rendelkezésre, kérjen ajánlatot a Bio-Science Kft.-től!
- IDT is the industry standard for both ligation-based and PCR-based indexing solutions
- A comprehensive offering of high purity adapters and primers
- Trusted customer support
- Complete customizability
Table 1. Recommended adapters and indexing primers compatibility based on library prep method.
| Full-length adapters | Indexing primer options | |||||
|---|---|---|---|---|---|---|
| Indexing strategy | UDI + UMI | UDI | CDI | Normalase-UDI | Normalase-CDI | |
| 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 | ✓ | |||||
*Note: the "UNI kit supports indexing by ligation, so either full-length (UDI-UMI) or stubby adapter + UDI primers can be used. All other library prep kits only support indexing by PCR
For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.
Considerations when selecting an adapter and primer design
IDT provides extensive solutions for stocked indexing solutions. Adapters are available with single index, unique dual index (UDI), and unique molecular identifiers (UMI) found in the IDT xGen UDI-UMI indexes (Figure 1). In addition, the adapters can be designed to include:
- Index lengths of 8 nt or 10 nt
- Combinatorial or unique dual indexes (CDI or UDI)
- Multiplex capacity up to 1536 unique indexes
- Indexing primers designed for performing enzymatic library normalization using our proprietary NormalaseTM technology.
In addition to the stocked products, IDT provides the ability for even greater flexibility and control, by using the Custom Adapter Configurator tool to guide you through designing your own Custom NGS Adapters.
Figure 1. Examples of adapter designs. A variety of NGS adapter designs are available from IDT. When selecting or designing adapters, consideration must be given to the intended application, multiplexing needs, specification requirements, and analysis methods.
Sample indexing
Sample indexes (or indices) enable multiple samples to be sequenced together (i.e., multiplexed) on the same instrument flow cell or chip. Each sample index, typically 8–10 bases, is specific to a given sample library and is used for de-multiplexing during data analysis to assign individual sequence reads to the correct sample. Predesigned indexes from IDT are balanced to prevent GC bias and color-balanced for 2- and 4-color Illumina instruments. Adapters and primers may contain single or dual sample indexes depending on the number of libraries combined and the level of specification desired. Illumina recommends using unique dual indexes (UDIs) as a method to mitigate errors introduced by index-hopping. UDIs are particularly important when using instruments with patterned flow cells, such as the NovaSeq® system from Illumina.
IDT provides several indexing options with its Custom NGS Adapters. These include both IDT and Illumina 8- and 10-base index series, as well as the ability to upload your own index files.
Molecular barcoding
Unique molecular identifiers (UMIs) provide reliable error correction. UMIs are short sequences that incorporate a unique barcode onto each molecule within a given sample library.
- UMIs are used to identify PCR duplicates. PCR duplicates created during library amplification steps will share the same insert and UMI tag.
- UMIs have also been shown to reduce the rate of false-positive variant calls and increase variant detection. By incorporating individual barcodes on each original DNA fragment, variant alleles present in the original sample (true variants) can be distinguished from errors introduced during library preparation, target enrichment, or sequencing. Any identified errors can be removed by bioinformatics methods before final data analysis.
Adapters that contain UMIs, such as the xGen UDI-UMI Adapters, are available with a UDI design for identification of low-frequency variants. IDT Custom NGS Adapters can also be configured with UMIs.
Adapter manufacturing
Stringent manufacturing methods are critical for producing high-quality NGS adapters. Substandard manufacturing practices can lead to low purity adapters or adapter cross-contamination, either of which will negatively impact sequencing results. The IDT proprietary TruGradeTM process uses state-of-the-art synthesis and purification methods, designed specifically for NGS adapters. IDT also offers GMP ISO 13485 grade adapter manufacturing for clinical research applications.
In addition to stringent manufacturing methods, IDT also performs functional NGS testing on each new batch of stocked adapter and indexing primer products to ensure they produce sequencing libraries that meet our high-quality standards.
Our leadership in NGS adapter synthesis made us the clear choice when Illumina sought a partner to develop the next generation of indexed adapters to improve sample multiplexing. These adapters contain Illumina’s unique dual indexes (UDIs), which mitigate sample misassignment due to index hopping. We manufacture UDI adapters for Illumina and are also licensed to sell your own custom designs containing these UDI sequences.
For more information, or to order custom adapters, please contact our Technical and Customer Support.
| Indexing Option | xGen UDI-UMI Adapters | xGen Stubby Adapter and UDI Primers | xGen Normalase UDI Primers | xGen UDI Primers | xGen Normalase CDI Primers | xGen CDI Primers | Custom NGS adapters |
|---|---|---|---|---|---|---|---|
| Configuration | UDI-UMI | UDI | UDI | UDI | CDI | CDI | single index, combinatorial dual indexing, UDI, or UDI-UMI |
| Sample index length | 8 base, unique sample indexes | 8 base, unique sample indexes | 10 base, unique sample indexes | Both 8 and 10 base available, unique sample indexes | 8 base indexes | 8 base indexes | Configurable |
| Concentration | 15 µM | 15 µM (Stubby adapter), 10 µM ( each primer) |
Proprietary | 20 µM total (10 µM each Primer)
|
Proprietary | 12uM total (6uM each primer after arraying) | 15 µM (Adapter), 20 µM total (10 µM each Primer) |
| Shipping container | 96-well plates, single use | Tubes (Stubby Adapter), Single-use plates (Primers) |
96-well plates, single use | 96-well plates, single use UDI 10nt Primers (2nm) plates are bulk/multi-use |
Tubes for each i7 and i5 index | Tubes for each i7 and i5 index | Tubes, Matrix® plates†, or single-use plates |
| Reactions | 1 reaction per adapter | 1 reaction per primer pair | 1 rxn per primer pair | 1 rxn per primer pair for 96-well plates, single use | 1 rxn per primer pair | 1 rxn per primer pair | Varies |
| Illumina platform compatibility | 2- and 4- color systems | 2- and 4- color systems | 2- and 4- color systems | 2- and 4- color systems | 2- and 4- color systems | 2- and 4- color systems | Designs for any application |
Choose from a variety of options that personalize the adapters to your NGS workflow for Illumina sequencing. Order Custom NGS Adapters when you need to:
- Scale up your experiments—get the delivery format (volume, plate, single-use) and volume-pricing that best suit your NGS study.
- Expand your set of barcodes to increase sample throughput—augment limited sets of stocked adapters. Our design tool will support uploading up to 2000 custom index sequences!
- Supplement commercial library kit components—create your own custom library prep workflow that fits your experimental design.
The Custom Adapter Configurator tool helps you design the adapters best suited to your experiments by walking you through these choices:
- Library prep method
- Configuration (SI, CDI, UDI, UDI-UMI)
- Attachment style
- Indexing strategy
- Number of indexes
- Size (reaction number or nmol)
- Delivery format (tubes, plates)
- Methylated/unmethylated
- TruGradeTM processing
Table 2. Suggested barcode configuration based on NGS application.
| Application | Best choice | Alternatives |
|---|---|---|
| Germline characterization SNPs, indels, crude CNV; no concern of sample crosstalk |
UDI | SI, CDI, or UDI-UMI |
| Germline characterization where sample crosstalk is important Translational research, inherited genetics, infectious disease research |
UDI | UDI-UMI |
| Low-level mutation detection, down to ~1% frequency Cancer, mosaicism, other diseases where somatic mutations are important |
UDI-UMI |
xGen™ Normalase™ Module
Core kit for performing Normalase, includes Normalase I and Normalase II reagents and Normalase terminal primers, Normalase indexing primers sold separately.
xGen™ Normalase™ CDI Primers
Combinatorial dual index primers designed for Normalase workflow. Consists of 20 individual tubes of indexes that support up to 96 combinations of i7-i5 indexes.
xGen™ Normalase™ Terminal Primers
Premixed primers for conditioning Normalase™ libraries to ensure the necessary sequence motifs are present on the library fragments, for use in the Normalase™ workflow. This is included in the Normalase™ Module.
xGen™ Stubby Adapter
Standalone stubby adapter for TA-ligation library preparation workflows, where sample indexing by PCR is preferred. Sample indexing is performed using any of the IDT xGen™ indexing primer products (sold separately). This stubby adapter is intended for customers using non-IDT library prep kits that utilize TA ligation for library construction. This module is not required to be purchased separately when using the IDT xGen™ Library Prep Kits.
xGen™ Stubby Adapter and UDI Primers
Stubby adapter and unique dual index primer pairs for TA-ligation library preparation workflows where indexing by PCR is preferred. These are delivered as single-use plates containing either 16 or 96 primer pairs, and a separate tube of stubby adapter with a matching number of reactions.
xGen™ UDI Primer Pairs
Premixed unique dual index primer pairs for sample indexing by PCR. These are delivered as single-use plates containing either 16 or 96 primer pairs, or for high-volume/high-throughput customers we have bulk 2 nmol offerings of primer with 10 nt indexes. The 10 nt indexes are available in sets of 384, 768, and 1536 index pairs. All plates except the bulk 2 nmol offerings are single-use to minimize the risk of contamination by multiple handling events.
Legacy Swift Indexing Primers
Legacy Swift Primers, CDI and UDI indexing strategies. The xGen™ CDI Primers are individual tubes of indexes, to be arrayed in a combinatorial fashion for up to 96 possible barcode combinations, and the xGen™ UDI Primers, Plate 2 are premixed Unique Dual Index primers in single-use plates. Both products have 8nt barcodes. Note that these primers are not compatible with any other IDT indexing primers, due to potential demultiplexing issues.
xGen™ UDI-UMI Adapters
Full-length adapters with unique dual indexes and optional unique molecular identifiers for sensitive NGS applications. Utilizes TA ligation workflow for incorporating sample indexes during the ligation step.
TruSeqTM–Compatible Full-length Adapters
Each sequence design includes duplexed adapters, delivered in Duplex Buffer (IDT), and available in tubes or plates.
TruSeqTM–Compatible Stubby Adapter and Indexing Primers
Each sequence design includes duplexed adapters designed to be compatible with ligation-based library prep, delivered in Duplex Buffer (IDT) and provided in tubes, as well as a primer mix delivered in IDTE (1X TE), pH 8, available in plates.
NexteraTM –Compatible Indexing Primers
Each sequence design includes a primer mix designed to be compatible with transposase-based library prep, delivered in IDTE (1X TE), pH 8, available in plates.
TruSeqTM–Compatible Indexing Primers
Each sequence design includes a primer mix designed to be compatible with ligation-based library prep, delivered in IDTE (1X TE), pH 8, available in plates.
xGen™ NGS Adapter Buffer
For dilution and storage of duplexed NGS adapters and/or stubby adapter.
xGen™ Library Amplification Primer Mix
Premixed P5/P7 primer pairs to amplify indexed NGS libraries, to achieve the necessary yield for sequencing. Available in three reaction sizes, for flexibility.
