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Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Ion Torrent™)

The new Ion Xpress™RNA-Seq Barcode 1-16 Kit provides a set of 16 unique barcode primers for sequencing RNA on the Ion Torrent PGM™semiconductor sequencer. When used in combination with the Ion Total RNA-Seq Kit v2, the Ion Xpress™RNA-Seq Barcode 1-16 Kit enables users to pool up to 16 fragment libraries prior to template preparation and then conduct multiplexed sequencing analysis, simplifying the Ion semiconductor sequencing workflow for small and whole transcriptome RNA.

Features and Benefits:
• Efficient multiplexing-enables multiplexing of up to 16 fragment libraries on a single sequencing chip
• Both sequence- and flow-optimized for equal representation of all barcodes in a pool
• Multiplexing decreases the cost and the handling requirements of template preparation and sequencing
• Robust error correction built in by design for added confidence in sample identification

Efficient Multiplexing with Barcode Primers Enables Higher Throughput Sample Sequencing
Multiplexing with barcoded libraries leads to more cost-effective runs by permitting up to 16 samples per run, significantly decreasing the cost and handling requirements of template preparation and sequencing.

Sequence- and Flow-Optimized for Increased Performance and Efficiency
Barcode primers contain sequences that are optimized to provide equal representation of all barcodes in a pool, require a minimum number of flows to interrogate, and necessitate only 20 bases of barcode and adaptor sequencing, which results in more economical multiplexed sequencing runs.

Robust Error Correction Built In By Design
Built-in error correction significantly minimizes the possibility of incorrect sample assignment.

The Ion Xpress™ RNA-Seq Barcode 01-16 Kit is designed to create 10 multiplexed libraries per barcode or a total of 160 multiplexed libraries.

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.

Ion Total RNA-Seq Kit v2 (Ion Torrent™)

The Ion Total RNA-Seq Kit v2 includes the reagents needed to prepare representative cDNA libraries for strand-specific RNA sequencing on the Ion Proton™ or the Ion Personal Genome Machine® (PGM™) systems. The Ion Proton™ System is ideally suited for sequencing the whole transcriptome (ribosomal RNA depleted or polyA), while the Ion PGM™ System is suitable for small RNA, as well as viral and bacterial transcriptomes. Either small RNA (such as microRNA) or whole transcriptome RNA samples can be prepared for next-generation sequencing using the Ion Total RNA-Seq Kit v2. Version 2 of the Ion Total RNA-Seq Kit is an improvement over the first generation kit. The gel size selection step in the small RNA workflow has been replaced with a magnetic bead-based method. Magnetic bead-based purification replaces all of the filter cleanup steps and the total reaction time has been reduced to 6 hours.

Additional Features of the New Ion Total RNA-Seq Kit v2:

• Greater accuracy—SuperScript® VILO™ and Platinum® PCR SuperMix High Fidelity added for highest template fidelity
• Barcode compatible—works with Ion Xpress™ RNA-Seq Barcode 01-16 Kit for multiplexing
• Automation friendly—magnetic bead-based purification simplifies automation of library construction

As with the previous kit, the Ion Total RNA-Seq Kit v2:

• Preserves strand information—all mapped reads are aligned in the direction of transcription relative to the chromosomal strand
• Allows you to choose your workflow—interrogate either small RNA or the whole transcriptome
• Allows you to analyze any type of RNA—supports small RNA, rRNA depleted total RNA, and poly(A) RNA

The Ion Total RNA-Seq Kit v2 is designed to make cDNA library preparation for the Ion Proton™ and PGM™ systems fast and flexible. It can be used to generate a representative cDNA library, flanked by specific sequences necessary for sequencing, from any type of RNA sample.

Designed as a complete solution with a common workflow, the Ion Total RNA-Seq Kit v2 combines optimized reagents and protocols for discovery of small RNAs and isoforms, coding RNA, noncoding RNA, and alternative splice variants.

Small RNA Analysis
During small RNA library construction, the 3' and 5' adaptors are attached directionally and simultaneously. As a by-product of this step, an adaptor:adaptor product may be formed without an RNA insert. This byproduct will amplify during first strand synthesis and PCR. If not removed, > 50% of the reads will be the adaptor dimer. Historically, the only way to separate the adaptor dimer from the wanted small RNA containing library fragments has been through gel size selection. The Ion Total RNA-Seq Kit v2 uses proprietary technology to inhibit cDNA synthesis of the adaptor byproduct, thus allowing cDNA separation with magnetic bead-based technologies. Total reaction time has been reduced from 1.5 days to approximately 6 hours. A separate Magnetic Bead Cleanup Module is included with the kit. Additional modules may be purchased separately.

Start with total RNA containing as little as 5–100 ng of miRNA, or RNA enriched for small RNA containing 1–100 ng of miRNA. The small RNA protocol provides guidance on whether to start with total RNA or RNA enriched for small RNA, based on the small RNA content of your sample. Small RNA enrichment protocols are also provided.

Whole Transcriptome Analysis
The whole transcriptome protocol enables construction of strand-specific libraries in approximately 5 hours. Starting with as little as 100 ng of total RNA, construct a library from 1 ng of poly(A) RNA or 25 ng of rRNA-depleted RNA following the RNA enrichment and library generation protocols provided in the manual. Because the libraries are not limited to cDNA derived only from poly(A) RNA, Ion Total RNA-Seq Kit libraries support a more thorough investigation of transcriptome complexity, capable of characterizing known and undocumented transcripts, including alternative splice variants, fusion transcripts, and SNPs.

Preserve Strand Information
Unlike methods that ligate adapters to double-stranded cDNA, the Ion Total RNA-Seq Kit v2 utilizes proprietary Ambion® technology to attach the adapters in a directional manner that preserves strand information in the resulting libraries. In addition, both the 3' and 5' adapters are attached simultaneously, reducing ligation and clean-up steps.

Preserving strand orientation during library construction helps enable more accurate determination of the structure and expression level of transcripts, and can aid in the discovery of novel transcription regions from both the positive and negative genomic strands.

The Ion Total RNA-Seq Kit v2 is designed to create RNA libraries from up to 12 samples for small RNA or whole transcriptome sequencing on the Ion Proton™ or PGM™ systems.

Ion Plus Fragment Library Kit for AB Library Builder™ System (Ion Torrent™)

The Ion Plus Fragment Library Kit for AB Library Builder™ System provides a rapid, flexible, and high-throughput solution for library construction upstream of semiconductor sequencing when starting with fragmented DNA. This ready-to-use reagent cartridge simplifies next-generation sequencing by enabling automated DNA fragment library preparation for the Personal Genome Machine® and soon the Proton™ sequencing systems.

This kit contains sample preparation reagents for library construction of 13 DNA libraries for semiconductor sequencing. Use of this reagent cartridge requires additional standard or barcoded library adapters (sold separately).

This library kit offers:

Simplicity and convenience of automated library preparation upstream of semiconductor sequencing
Rapid and flexible workflow automating library creation and size selection in as little as 2 hours starting with pre-fragmented DNA
Lower input requirement providing the ability to make amplification-free libraries from as little as 50 ng starting material
Scalable methodology applicable to automated library preparation systems including the AB Library Builder™ System

With greatly reduced hands-on time, the Ion Plus Fragment Library Kit for AB Library Builder™ System automates preparation of up to 13 standard, paired-end, or barcode fragment libraries in about 2 hours per run, starting with small amplicons or pre-sheared gDNA samples. Size selection of the libraries is performed automatically without the expense or effort of gel-based methods. Alternatively, libraries can be manually size-selected by conventional methods after the automated run.

Starting with 50–1000 ng of input DNA, the kit yields significantly higher amounts of library than current manual methods, eliminating the need for PCR amplification (i.e. "amplification-free" libraries) for most sequencing needs.

A Single-Day Workflow: The Next Stage in a Sequencing Revolution
With the ability to prepare up to 13 libraries in a little over 2 hours, the Ion Plus Fragment Library Kit for AB Library Builder™ System is a key step towards automation of the Ion sequencing workflow, making comprehensive analyses of your sample(s) of interest more convenient than ever before. This modular reagent system allows for the construction of a variety of fragment libraries (i.e., standard and barcoded) depending on the library adapters used (library adapters sold separately).

Ion Torrent Sequencing Made Simpler, Faster, and More Affordable
The Ion Plus Fragment Library Kit for AB Library Builder™ System automates library creation and size selection, eliminating the need for costly time-consuming gel-based size selection, and requires as little as 50 ng of sample, accelerating your path to semiconductor sequencing. This automated library preparation solution provides fast and scalable workflows for sequencing projects requiring low- to high-throughput processing capabilities.

For Research Use Only. Not for human or animal therapeutic or diagnostic use.

Ion PGM™ Hi-Q™ View Chef Kit (Ion Torrent™)

The Ion PGM™ Hi-Q™ View Chef Kit enables accurate and reproducible template preparation, chip loading, and sequencing of 200 bp libraries on the Ion Chef™ System and the Ion PGM™ System. The plug-and-play, pre-packaged, single-use reagent cartridges enable a fully automated workflow, processing two samples per run for increased productivity. Reagent and sample barcoding features help to verify the user-defined run plan and offer complete run traceability.

• Delivers automated template preparation and chip loading for 200 bp libraries
• Provides the most accurate sequencing chemistry available for the Ion PGM System
• Designed to minimize the hands-on time required to prepare your samples
• Helps increase lab throughput with dual sample processing

Maximize your results with high-accuracy sequencing chemistry
The Ion PGM Hi-Q View Chef Kit is an integral component of the Ion Torrent™ next-generation sequencing workflow. Designed to simplify the overall workflow with minimal hands-on time, the Ion Chef System is ideal for users of all experience levels. The Ion PGM Hi-Q View Chef Kit contains the most advanced templating and sequencing chemistries available to Ion PGM customers. Use the Ion PGM Hi-Q View Sequencing Kit to help maximize your variant calling performance and improve de novo sequencing applications.

A single kit to meet your Ion PGM sequencing needs
The Ion PGM Hi-Q View Chef Kit is configured to support all of your sequencing needs for applications requiring 200 bp read lengths. This kit supports the Ion 314™ Chip v2 BC, Ion 316™ Chip v2 BC, and the Ion 318™ Chip v2 BC. The kit includes sufficient reagents for eight 200 bp sequencing reactions.

For 400-base applications, order the Ion PGM™ Hi-Q™ View Chef 400 Kit (Cat. No. A30798), which provides all the reagents needed for eight 400 bp sequencing reactions.

Collibri™ PS DNA Library Prep Kit for Illumina Systems, with CD indexes (Invitrogen™)

The Invitrogen Collibri PS DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems. The kit is suitable for physically sheared (PS) genomes of all sizes and variable quality, including FFPE samples.

The Collibri PS DNA Library Prep Kit:
• Includes in-process visual feedback at every step of the process to confirm proper mixing of reagents for the highest chance of library prep success
• Includes all necessary components in a single kit
• Offers consistent, even coverage of variable GC regions from inputs ranging from 1 to 1,000 ng
• Offers improved coverage of challenging genomic regions compared to already available library prep technologies
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PS DNA Library Prep Kit contains inert dyes that provide visual feedback during library preparation: the reaction mixes change color in response to the addition of critical components at each step. The inert dyes do not interfere with enzymatic reactions and do not compromise sequencing results.

The Collibri PS DNA Library Prep Kit consistently offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from a wide range of inputs (1 ng to 1 µg) of physically sheared double-stranded DNA (see figure below). Additionally, a PCR-free version is offered for inputs starting at 500 ng DNA. The entire library preparation protocol takes about 3.5 hours with a PCR workflow. The kit contains adapters with unique dual indexes (UDIs) or combinatorial dual indexes (CDs) that allow pooling of up to 24 or 96 different samples before the sequencing run.

Applications
The Collibri PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

BigDye™ Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems™)

The BigDye® Terminator v3.1 Cycle Sequencing Kit's robust, highly flexible chemistry is ideal for de novo sequencing, resequencing, and finishing with PCR product, plasmid, fosmid, and BAC templates.

• Improve the quality of your results for a wide range of sequencing applications
• Optimized for long read lengths
• Better dye mobility characteristics
• Improved performance reading through GT-rich regions
• Get longer, higher-quality reads with more uniform peak heights and optimal signal balance
• Enhance your productivity and reduce costs

Get more uniform peak heights and improved accuracy
With BigDye® Terminator v3.1 kit superior chemistry, you generate data with uniform peak heights and optimized signal balance. This results in longer, higher-quality reads and more accurate base assignments for heterozygote and mutation detection.

SGS™ All Species ID Food DNA Analyser Kits (Thermo Scientific™)

Identify meat, plant or fish species present in all food sample types with ready-to-use DNA test kits, software and Ion Torrent NGS technology.

Ion 510™ & Ion 520™ & Ion 530™ Kit – Chef (1 sequencing run per initialization) (Ion Torrent™)

The Ion 510 & Ion 520 & Ion 530 Kit-Chef (1 sequencing run per initialization) enables robust and automated template preparation and sequencing of up to 400 base-read libraries using the Ion Chef System and the Ion S5 or Ion S5 XL sequencing system. The Ion 510 & Ion 520 & Ion 530 Kit contains pre-packaged single-use template and sequencing reagent cartridges with integrated sample tracking, delivering an automated workflow for sequencing of 8 loaded chips with complete run traceability. This kit accommodates 1 sequencing run per initialization. For 2 sequencing runs per initialization (200 base-read applications only), see Cat. No. A34461.

The Ion 510 & Ion 520 & Ion 530 Kit-Chef workflow:
• Provides template preparation and chip loading reagents for up to 400 base-read libraries
• Simplifies your research with ready-to-use, disposable reagent cartridges for sequencing
• Enables fast and simple sequencing instrument set-up, with less than 15 minutes hands-on time
• Leverages the latest advancements in data quality and accuracy
• Maximizes flexibility with compatibility for the Ion 510, Ion 520, and Ion 530 chips

The Ion S5 and Ion S5 XL sequencers, along with the Ion Chef System, offer reproducible sequencing workflows, with minimal hands-on time. Choose to pair the Ion 510 & Ion 520 & Ion 530 Kit with the Ion 510 Chip Kit (up to 3 million reads per chip), the Ion 520 Chip Kit (up to 5 million reads per chip), or Ion 530 Chip Kit (up to 20 million reads), allowing for flexibility of total throughput. For even greater flexibility, combine different chip types in a single Ion Chef run when using Torrent Suite Software 5.6 and above. For de novo research applications, add the Ion S5 Calibration Standard to prepared libraries for improved base-calling accuracy.

Ion Xpress™ Plus Fragment Library Kit for AB Library Builder™ System (Ion Torrent™)

The Ion Xpress™ Plus Fragment Library Kit for AB Library Builder™ System provides a rapid, flexible, and high-throughput solution for library construction upstream of the semiconductor sequencing workflow. This ready-to-use reagent cartridge simplifies next-generation sequencing by enabling automated DNA fragment library preparation for the Personal Genome Machine® and soon the Proton™ sequencing systems.

This kit contains sample preparation reagents for enzymatic shearing and library construction of 13 DNA libraries for semiconductor sequencing. Use of this reagent cartridge requires the addition of library adapters (sold separately).

This library kit offers:

Simplicity and convenience of automated library preparation upstream of semiconductor sequencing
Superior coverage uniformity for diverse sample types using our proprietary Ion Shear™ Plus chemistry
Lower input requirement providing the ability to make amplification-free libraries from as little as 50 ng of starting DNA
Rapid and flexible workflow producing Ion fragment libraries containing user-selectable and automatically size-selected insert sizes of 100–400 bp in as little as 2 hours
Significant cost savings by removing the need for ancillary shearing devices and size-selection gels
Scalable methodology to meet high-throughput sequencing requirements

With its plug-n-play modular reagent design, this revolutionary kit automates all steps of library creation, including both DNA fragmentation and library size selection, in as little as 2 hours with limited set-up time and minimal subsequent user-intervention. DNA fragmentation is automated with enhanced, proprietary Ion Shear™ DNA fragmentation chemistry to achieve user-selectable inserts of 100–400 bp in length. Size selection of the libraries is performed automatically without the expense or effort of gel-based methods. Alternatively, libraries can be manually size-selected using conventional methods after the automated run. Starting with 50–1000 ng of input DNA, the kit yields significantly higher amounts of library than current manual methods, eliminating the need for PCR amplification (i.e., "amplification-free" libraries) for most sequencing needs.

A Single-Day Workflow: The Next Stage in a Sequencing Revolution
With the ability to prepare up to 13 libraries in a little over 2 hours, the Ion Xpress™ Plus Fragment Library Kit for AB Library Builder™ System is a key step towards automation of the Ion sequencing workflow, making comprehensive analyses of your sample(s) of interest more convenient than ever before. Furthermore, Ion Xpress™ Plus fragment libraries generated using the AB Library Builder™ system exhibit the superb coverage uniformity typically seen with proprietary Ion Shear™ DNA fragmentation chemistry and higher recovery rates than other library construction methodologies. So you can be confident of generating the best data in the shortest time, without the hassle or expense of manual shearing and size selection.

Ion Torrent Sequencing Made Simpler, Faster, and More Affordable
Ion Shear™ Plus DNA fragmentation technology eliminates the need for costly physical shearing devices for most applications and requires as little as 50 ng of sample, accelerating your path to semiconductor sequencing. This flexible technology also provides users the ability to adjust fragmentation and size-selection sizes to accommodate a range of sequencing read lengths depending on their project requirements. This automated library preparation solution provides fast and scalable workflows for sequencing projects requiring low- to high-throughput processing capabilities.

For Research Use Only. Not for human or animal therapeutic or diagnostic use.

Ion S5™ Precision ID Chef & Sequencing Kit (1 run per initialization) (Applied Biosystems™)

The Ion S5 Precision ID Chef & Sequencing Kit enables robust and automated template preparation and sequencing of Precision ID libraries using the Ion S5 worfklow (eight initializations and eight sequencing runs). This kit provides template preparation and chip loading reagents for libraries generated with commercially available Precision ID panels (GlobalFiler NGS STR Panel v2, Identity Panel, Ancestry Panel, mtDNA Whole Genome Panel, and mtDNA Control Region Panel). For four initializations and eight sequencing runs, see Cat. No. A33208.

The Ion S5 Precision ID Chef & Sequencing Kit for the Ion Chef and Ion S5/Ion S5 XL workflow:
• Provides template preparation and chip loading reagents for Precision ID libraries
• Simplifies your testing with ready-to-use, disposable reagent cartridges for sequencing
• Delivers fast and simple sequencing instrument set-up, with less than 15 minutes hands-on time
• Leverages our latest advancements in data quality and accuracy
• Maximizes flexibility through compatibility with both the Ion 520 and Ion 530 chips

The Ion S5 and Ion S5 XL sequencers, along with the Ion Chef System, provide reproducible sequencing workflows with minimal hands-on time. Choose to pair the Ion 520 & Ion 530 Kit with the Ion 520 (up to 5M reads) or Ion 530 (up to 20M reads) Chip kit, allowing for flexibility of total throughput.

Collibri™ PS DNA Library Prep Kit for Illumina Systems, with UD indexes (Set B, 25-48) (Invitrogen™)

The Invitrogen Collibri PS DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems. The kit is suitable for physically sheared (PS) genomes of all sizes and variable quality, including FFPE samples.

The Collibri PS DNA Library Prep Kit:
• Includes in-process visual feedback at every step of the process to confirm proper mixing of reagents for the highest chance of library prep success
• Includes all necessary components in a single kit
• Offers consistent, even coverage of variable GC regions from inputs ranging from 1 to 1,000 ng
• Offers improved coverage of challenging genomic regions compared to already available library prep technologies
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PS DNA Library Prep Kit contains inert dyes that provide visual feedback during library preparation: the reaction mixes change color in response to the addition of critical components at each step. The inert dyes do not interfere with enzymatic reactions and do not compromise sequencing results.

The Collibri PS DNA Library Prep Kit consistently offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from a wide range of inputs (1 ng to 1 µg) of physically sheared double-stranded DNA (see figure below). Additionally, a PCR-free version is offered for inputs starting at 500 ng DNA. The entire library preparation protocol takes about 3.5 hours with a PCR workflow. The kit contains adapters with unique dual indexes (UDIs) or combinatorial dual indexes (CDs) that allow pooling of up to 24 or 96 different samples before the sequencing run.

Applications
The Collibri PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Ion AmpliSeq™ Sample ID Panel (Ion Torrent™)

The Ion AmpliSeq™ Sample ID Panel is a versatile, cost effective, and easy-to-use human SNP genotyping panel comprising 9 specially designed primer pairs that can be added to the multiplex PCR reaction to generate a unique ID during post-sequencing analysis of research samples.

Designed to advance clinical research, the Ion AmpliSeq™ Sample ID Panel helps reveal sample misidentification for increased confidence during data analysis and reporting. The Ion AmpliSeq™ Sample ID Panel can be used in conjunction with any Ion AmpliSeq™ ready-to-use panel or custom panel designed via the Ion AmpliSeq™ Designer (www.ampliseq.com).

Verify Various Sample Combinations:

• Tumor/normal paired samples
• Samples from the same individual in longitudinal studies
• Multi-tissue or multi-tumor samples from the same individual

Sample Identification Through SNP Genetyping

• 8 primer pairs target 8 validated SNPs1
• Selected SNPs are unlinked, non-exonic markers that exhibit exceptional robustness and represent high minor-allele frequency in all human populations
• An additional primer pair targets the amelogenin gene, allowing quick gender determination
• The first letter of the Sample ID code provides instant gender determination for the sample
• Optimal discrimination power (~1:5,000*) with minimal sequencing needed

Simple Workflow—Just One Pipetting Step

• Spike 1 µL of the 20X Sample ID primer pool directly into any Ion AmpliSeq™ primer pool for co-amplification and downstream sequencing and data analysis
• Enabled for use with any Ion Xpress™ barcode
• Compatible with the Ion Reporter™ Software, a cloud-hosted software tool for automated variant analysis

Includes:
20X Ion AmpliSeq™ Sample ID Primer Pool

Required:
Torrent Suite Software (v3.0 or greater) that includes the Ion AmpliSeq™ Sample ID Panel plug-in
Ion AmpliSeq™ Library Kit 2.0 User Guide
Ion AmpliSeq™ ready-to-use panel or custom panel designed via the Ion AmpliSeq™ Designer (www.ampliseq.com)

1Pakstis AJ et al. SNPs for a Universal Individual Identification Panel. Hum Genet. 2010 Mar; 127(3):315-24.
*4641 discrimination power calculations assumes no missing genotyping data

Ion AmpliSeq™ Library Kit Plus (Ion Torrent™)

The Ion AmpliSeq Library Kit Plus is designed for rapid preparation of amplicon libraries using Ion AmpliSeq panels. Ion AmpliSeq technology enables scalable, multiplex polymerase chain reactions (PCR) from 12- to 24,000-plex in a single well. Next-generation sequencing (NGS) libraries can be prepared using as little as 1 ng of starting material.

Key product features:
• Scalable and efficient library preparation
• Easy and robust protocol
• Barcoded sample multiplexing

Scalable and efficient library preparation
Using as little as 1 ng of starting material, highly multiplexed PCR amplification of thousands of genomic target regions yields superior coverage uniformity and specificity, without the need of a specialized microfluidics PCR platform. The primers contain proprietary modifications that enable removal of primer sequences during library preparation, thereby resulting in efficient target assessment during sequencing.

Easy and robust protocol
The Ion AmpliSeq Library Kit Plus uses a plate-based format for easier sample handling and tracking, and for compatibility with automation and high-throughput laboratories. The protocol is simple to use and enables high yield and uniformity, reliably and reproducibly. The resulting libraries are ready for downstream template preparation using the automated Ion Chef System (which also provides the option of automated library preparation using the Ion AmpliSeq Kit for Chef DL8) or the Ion OneTouch 2 System followed by sequencing. The intuitive Torrent Suite Software and optional Ion Reporter Software enables automation of data analysis.

Barcoded sample multiplexing
The Ion AmpliSeq Library Kit Plus includes reagents for generating amplicons using Ion AmpliSeq primers and preparing libraries from the resulting amplicons. The kit enables the preparation of barcoded libraries using Ion Xpress Barcode Adapters 1-96 kits or IonCode Barcode Adapters 1-384 kits. Barcoded libraries can be combined and loaded onto a single Ion chip to minimize the sequencing run time and cost, and to allow for accurate sample-to-sample comparisons.

SOLiD™ RNA Barcoding Kit, Module 33-48 (Applied Biosystems™)

The SOLiD™ RNA Barcoding Kit, Module 33-48 enables you to increase the power of your studies by cost effectively increasing the numbers of samples analyzed in one SOLiD™ Sequencing run. Compatible with the SOLiD™ Total RNA-Seq Kit and SOLiD™ SAGE™ Kit, the SOLiD™ System barcodes contain unique sequences designed for optimal multiplexing. Module 33-48 contains sixteen different barcodes, selected for uniform melting temperature, low error rate, and orthogonal sequences that are unique in color space. The barcodes are added to the 3' end of the target sequence using a modified P2 adapter. SOLiD™ System barcoding enables the assignment of a unique identifier to templated beads made from a single library. Once the identifiers are assigned, multiple batches of templated beads may be pooled together for emulsion PCR and then sequenced.

Following sequencing, additional rounds of ligation-based sequencing are performed using primer sets complimentary to the barcode. The resulting reads can then be sorted by the barcode and aligned in groups to the reference sequence, enabling the sequencing of multiple libraries on the same slide—maximizing throughput while dramatically reducing costs.
SOLiD™ RNA Barcoding Kits contain PCR primer sets that are designed for use with the SOLiD™ Total RNA-Seq Kit and SOLiD™ SAGE™ Kit. Together, these kits enable multiplex SOLiD™ System sequencing of RNA samples. The SOLiD™ Total RNA-Seq Kit contains two primers:
• The SOLiD™ 5' PCR Primer is identical to the 5’ PCR primer provided in the SOLiD™ Total RNA-Seq Kit, and it contains the SOLiD™ emulsion PCR primer P1 sequence.
• The SOLiD™ 3' (reverse) PCR primers contain the P2 sequence required for SOLiD™ emulsion PCR, along with a unique barcode sequence, and an internal adaptor (IA) sequence necessary for sequencing the barcode (Figure 1). Using these primers in the cDNA amplification step of the SOLiD™ Total RNA-Seq Kit procedure generates barcoded cDNA libraries that can be mixed for multiplex SOLiD™ System sequencing.

Collibri™ PCR-free ES DNA Library Prep Kit for Illumina Systems, with CD indexes (Invitrogen™)

The Invitrogen Collibri PCR-Free ES DNA Library Prep Kit prepares libraries for whole genome sequencing (WGS) on high-throughput Illumina next-generation sequencing (NGS) systems.

The Collibri PCR-Free ES DNA Library Prep Kit:
• Includes in-process visual feedback at every step of the process to confirm proper mixing of reagents for the highest chance of library preparation success
• Includes all necessary components in a single kit
• Supports PCR-free protocols starting with as little as 100 ng of DNA
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PCR-Free ES DNA Library Prep Kit contains inert dyes that provide visual feedback of preparation progress: the reaction mixes change color in response to the addition of critical components at each step (see figure below for visual tracking). The inert dyes do not interfere with the enzymatic reactions and do not compromise the sequencing results.The Collibri PCR-Free ES DNA Library Prep Kit is designed for fast and convenient library preparation from inputs as low as 100 ng intact DNA. The entire library preparation protocol takes about two hours for the PCR-free workflow. The kit contains adapters with unique dual indexes (UDIs) or combinatorial dual indexes (CDs) that allow pooling of up to 24 or 96 different samples before the sequencing run.

Applications
The Collibri PCR-Free ES DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly