Shop All Library Preparation Kits for Sequencing

Ion AmpliSeq™ Transcriptome Human Gene Expression Kit Ion Torrent™

The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit enables the simultaneous measurement of the expression levels of over 20,000 human RefSeq genes in a single assay. Providing the ability to work directly with low input levels of total RNA derived from challenging samples such as formalin-fixed paraffin-embedded (FFPE) tissue or other samples with degraded RNA, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit is ideal for those interested in obtaining comprehensive, highly sensitive, and easily obtained gene expression measurements from a wide range of RNA sources.

The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit offers:
• Flexible, straightforward library preparation – start with as little as 10 ng of total RNA from FFPE samples, cells, or other sources
• Representation of over 20,000 human RefSeq genes
• Wider dynamic range and improved detection sensitivity compared to conventional microarray analysis
• A complementary software plug-in for automated sequencing analysis that provides gene quantitation and reporting as well as quality control metrics
• Compatibility with Ion Xpress™ Barcode adapters allowing for multiplexed sequencing

Wider dynamic range for enhanced performance
With a wider dynamic range and improved gene detection compared to conventional microarray analysis, the Ion AmpliSeq Transcriptome™ Human Gene Expression Kit provides a clear solution to researchers needing enhanced performance for their gene expression needs. A simple workflow allows for sample-to-gene quantitation in less than 2 days, helping to reduce workload and increase throughput.

Straightforward library preparation and multiplex sequencing
Starting with as little as 10 ng of total RNA, libraries can be prepared in approximately 7 hours with only one hour of hands-on time. Total RNA is first processed with the included SuperScript® VILO™ cDNA Synthesis kit, and the resulting cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all genes.

The resulting libraries are ready for downstream template preparation using the Ion OneTouch™ 2 System or Ion Chef™ System and sequencing on the Ion Proton™ sequencing system. Libraries can be barcoded for multiplexing, allowing for flexibility, helping to reduce cost, and increase throughput, with the recommended 16 libraries per Ion 550 Chip and 8 libraries per Ion 540 or Ion PI chip. Other multiplexing options are also possible, depending on the experimental design and desired level of sensitivity.

Automatic data analysis with Torrent Suite™ plug-in
Using the complementary analysis plug-in available with Torrent Suite™ software, gene quantitation information is automatically compiled, minimizing the requirement for costly computational resources and bioinformatics expertise to process raw sequencing data into meaningful information. An easy to interpret, highly portable table is produced containing all genes interrogated and their respective expression levels, output that may be used with a variety of existing software applications for downstream analysis of microarray or next-generation sequencing data.

Note: Libraries made from this protocol yield fragments suitable for 200-base read sequencing.

Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit Ion Torrent™

The Ion AmpliSeq Transcriptome Mouse Gene Expression Assay allows simultaneous gene expression measurement of over 20,000 mouse RefSeq genes in a single assay. Providing the ability to work directly with low input levels of total RNA, the Ion AmpliSeq Transcriptome Mouse Gene Expression Assay is ideal for those interested in obtaining comprehensive and highly sensitive gene expression measurements from a wide range of RNA sources. This particular kit enables manual library preparation with throughput flexibility. For automated production, see the Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit.

The Ion AmpliSeq Transcriptome Mouse Gene Expression Assay offers:
• Flexible, straightforward library preparation—start with as little as 10 ng of total RNA from tissues, cells, or other sources
• Fast gene expression profiling with simple workflow—go from RNA to data in <2 days with ~45 minutes of total hands-on time with the automated workflow of the Ion GeneStudio S5 and Ion Chef systems
• A complementary software plug-in for automated sequencing analysis that provides gene quantitation and reporting as well as quality control metrics
• Compatibility with Ion Xpress Barcode adapters, allowing for multiplexed sequencing

Leveraging the speed and simplicity of Ion AmpliSeq technology, this ultrahigh-multiplex PCR enrichment approach enables rapid gene expression profiling with minimal hands-on time. This research method provides a faster, simpler, and lower-cost sequencing method that is highly correlated to whole-transcriptome RNA sequencing.

Straightforward library preparation and multiplex sequencing with manual kit
Starting with as little as 10 ng of total RNA, libraries can be prepared in approximately seven hours with only one hour of hands-on time. Total RNA is first processed with the SuperScript VILO cDNA Synthesis Kit (not included), and the resulting cDNA is amplified using Ion AmpliSeq technology to accurately maintain expression levels of all genes.

The resulting libraries are ready for downstream template preparation using the Ion OneTouch 2 or Ion Chef System and sequencing on the Ion GeneStudio S5 or Ion Proton System. Libraries can be barcoded for multiplexing, providing flexibility, reduced cost, and increased throughput, with the recommended 16 libraries per Ion 550 Chip and 8 libraries per Ion 540 or Ion PI chip. Other multiplexing options are also possible, depending on the experimental design and desired level of sensitivity.

Oncomine™ Comprehensive Assay Plus, manual library preparation Ion Torrent™

The Oncomine Comprehensive Assay Plus is a targeted, next-generation sequencing (NGS) assay that provides a comprehensive genomic profiling solution appropriate for formalin-fixed paraffin-embedded (FFPE) tissues. The assay addresses multiple biomarkers associated with targeted and immune checkpoint therapies, covering over 500 genes, including comprehensive targets that are relevant in cancer. This version of the assay is designed for manual library preparation, not for automated library prepation using the Ion Chef System.

Features of the Oncomine Comprehensive Assay Plus include:
• Enables analysis of variants across 500+ genes
• Detection of SNVs, CNVs, InDels, TMB, MSI, and gene fusions
• Robust performance from as little as 10 ng per pool of nucleic acid isolated from FFPE samples including fine needle biopsies
• Characterized with molecular standards and controls
• Content driven by the Oncomine Knowledgebase and experienced scientists helps assure coverage of key targets aligned to published evidence

The Oncomine Comprehensive Assay Plus provides the reagents for library construction and four pools—two DNA and two RNA—of multiplex PCR primers for preparation of amplicon libraries from FFPE tumor samples. Designed to help you go from hundreds down to a few relevant cancer drivers, this assay is part of a comprehensive workflow that enables NGS data analysis from as little as 10 ng of nucleic acid per pool. The assay is optimized for sequencing on the Ion GeneStudio S5 systems with the Ion 550 Chip to enable up to four samples and a no-template control (NTC) per run. When combined with Oncomine Reporter Software, you can create reports that align labels, guidelines, and clinical trials to your results so you can focus on key drivers of cancer in your research.

From sample to answer
The Oncomine Comprehensive Assay Plus is part of an NGS workflow that helps researchers filter variant results from hundreds to just a few key cancer driver variants. Enabled by Oncomine Informatics, this filtering, as well as the annotations from on-market labels, established guidelines (US-NCCN, US-FDA, EMSO, EMA), and global clinical trials, helps you contextualize and interpret findings to move toward the answers you need.

Learn more about Oncomine Comprehensive Assay Plus ›

Oncomine™ TCR Beta-LR Assay Ion Torrent™

The Oncomine TCR Beta-LR Assay is designed to measure T cell diversity and clonal expansion by sequencing T cell receptor beta chain rearrangements. This assay utilizes a newly developed long-read sequencing technology on the Ion GeneStudio S5 next-generation sequencing systems. The assay kit provides a single pool of multiplex PCR primers, library reagents, and sample barcodes. Ion AmpliSeq libraries can be generated from research samples such as RNA extracted from whole blood, fresh-frozen tissue, or FACS-sorted cells.

Learn more about the assay ›

The assay is designed to efficiently capture all three complementarity determining regions of the TCR beta chain (CDR1, CDR2, CDR3) with high accuracy. It enables key applications such as predictive or prognostic biomarker discovery, T cell characterization, and identification of variable gene polymorphisms. The identification of rare and abundant clones can be achieved with a flexible RNA input amount of 10 ng (minimum) and up to 1 µg. The use of RNA template allows sequencing of productive and relevant variable (V), diversity (D), and joining (J) rearrangements—improving the identification of rare clones.

Note: Information about data analysis using Ion Reporter Software v5.6 can be found in the User Guide below.

Benefits of the Oncomine TCR Beta-LR Assay include:
• Long-read RNA sequencing (up to 400 bp amplicon length) comprehensively covering TCR beta chain
• Detection of clones over a wide dynamic range
• Unbiased output generated from Ion AmpliSeq technology
• Efficient workflow with 48 hr sample-to-results time
• Flexible input requirements ranging from 10 ng to 1 µg
• Compatibility with a variety of research sample types including fresh-frozen tissue, whole blood, and sorted cells
• Streamlined and user-friendly informatics solution with multi-sample analysis functionality

Why are immunologists and immuno-oncologists interested in T cell repertoire sequencing research?
• To characterize diversity and monitor features of T lymphocytes in blood and infiltrated tumors
• To identify variable gene polymorphisms implicated in autoimmune disease or immune-mediated adverse events
• To optimize the manufacture and function of therapeutic or engineered T cells

Unlike other technologies, the Oncomine TCR Beta-LR Assay offers:
• Long-read sequencing, enabling comprehensive coverage of TCR beta chain
• High accuracy and sensitivity through a superior multiplex PCR design
• Use of very low input RNA as a starting material (10 ng)
• High multiplexing and low cost per sample, enabling large-scale studies
• Accelerated discovery cycles through fast turnaround time

The entire workflow (figure below) from isolation of RNA to analysis of samples can be accomplished in two days using the Ion Chef templating system and the Ion S5 or Ion S5 XL sequencing system.

Precision ID Library Kit Ion Torrent™

The Precision ID Library Kit is designed for rapid preparation of amplicon libraries using HID-Ion AmpliSeq ready-to-use panels, for sequencing on Ion Torrent sequencing system. This kit uses only certain components found in the Ion AmpliSeq™ Library Kit 2.0, that are needed for Precision ID applications, making the Precision ID Library Kit more customized and specific for forensic research use only.

Key features:

Simple protocol
• 96 well plate-based workflow allows easy sample management
• No library amplification with qPCR quantification

Ion AmpliSeq™ HiFi Master Mix
• Enables cleaner amplification for increased coverage uniformity
• Up to 3,072-plex PCR allows larger panel designs

Digestion reagent
• Cleaner digest allows for more efficient downstream sequencing

Benefits for HID applications:

• 1 ng of DNA input is recommended for the Precision ID panels
• Less components to help save time and money by preventing unnecessary waste

Scalable multiplex PCR reactions
The Precision ID Library Kit is built on Ion AmpliSeq chemistry, which enables scalable multiplex PCR reactions from 12- to 3,072-plex in a single well using just 1 ng of starting DNA. Ion AmpliSeq panels and primer pools allow highly multiplexed PCR amplification of thousands of genomic target regions, with superior coverage uniformity and specificity, without the need of a specialized microfluidics PCR platform. In addition, the primers contain proprietary modifications that enable removal of primer sequences during library preparation, for efficient target assessment during sequencing. Multiple primer pools can be used to create overlapping amplicons that enable complete coverage of large targets.

Barcoded library preparation
The Precision ID Library Kit includes reagents for generating amplicons with 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 and the IonCode™ Barcode Adapters 1-384 Kit. Barcoded libraries can be combined and loaded onto a single Ion chip to minimize the sequencing run time and cost and allow for accurate sample-to-sample comparisons.

Easy and flexible protocol
The Precision ID Library Kit uses a plate-based format for easier sample handling and tracking, and for compatibility with automation and high-throughput laboratories.

The resulting DNA libraries are ready for downstream template preparation for clonal amplification on Ion Sphere™ particles using the automated Ion OneTouch™ 2 System. The intuitive Torrent Suite Software and HID SNP or STR Genotyper plug-ins enable you to go from extracted DNA to ancestry-informative genotypes in less than two days*.

*Using the Applied Biosystems™ Precision ID NGS System for Human Identification

Collibri™ Stranded RNA Library Prep Kit for Illumina™ Systems, with human/mouse/rat rRNA depletion kit and UD indexes Invitrogen™

The Invitrogen Collibri Stranded RNA Library Prep Kit for Illumina Systems is designed for robust construction of cDNA libraries for strand-specific RNA sequencing on Illumina next-generation sequencing (NGS) systems. The kit brings together the superior features of SuperScript IV Reverse Transcriptase, Dynabeads magnetic particles, and Platinum SuperFi DNA Polymerase, enabling users to obtain high-quality sequencing-ready libraries.

The Collibri Stranded RNA Library Prep Kit offers:
• Short, automation-friendly workflow— total RNA can be converted to sequencing-ready library within 6.5 hours
• Inert dyes in the reagents—see the progress of library generation without any negative effect on quality
• Superior rRNA removal
• Uniform transcript coverage and high transcript detection sensitivity
• High sensitivity of differential gene expression detection
• >98% strand specificity
• Efficient detection of non-coding RNA
• Preservation of 3‘ end sequence information

This Collibri Stranded RNA Library Prep Kit is designed for fast and convenient library preparation starting with sample inputs of 100 ng—1 µg of total human, mouse, or rat RNA. Single-tube adapter ligation and reverse transcription reactions, as well as magnetic bead-based rRNA depletion and library purification steps, enable completion of the entire workflow in approximately 6.5 hours. The kit is suitable for various-quality RNA samples, including FFPE samples.

Visual cues of process integrity
For maximum convenience, visual cues of process integrity are included throughout the library preparation workflow. Monitor progress of library generation using visual feedback from dyes in critical reagents. The reaction mix changes color in response to the addition of critical components at each step to ensure that library preparation has the highest chance of success. The inert dyes do not interfere with enzymatic reactions and do not compromise sequencing results.

How it works
The Collibri Stranded RNA Library Prep Kit with Human/Mouse/Rat rRNA Depletion Kit includes ribosomal RNA (rRNA) depletion reagents to enable a comprehensive view of the transcriptome through superior removal of human, mouse, and rat rRNA. Full-length Illumina-compatible adaptors are introduced by PCR amplification using Platinum SuperFi DNA Polymerase to construct single-indexed or unique dual-indexed libraries compatible with single-read or paired-end sequencing. The kit contains 24 or 96 either single-indexed barcoded PCR primers (i7) pre-mixed with a universal i5 primer or unique dual-indexed PCR primers that enable multiplexing of up to 96 libraries. Optimized cleanup steps efficiently remove residual primers and adapter/primer dimers while preserving high library yields.

A related product, the Collibri Library Quantification Kit, is recommended for qPCR-based quantifications of libraries before proceeding to sequencing.

Applications
The Collibri Stranded RNA Library Prep Kit is recommended for:
• Gene expression studies
• Alternative splicing analysis
• Non-coding RNA detection and discovery
• Identification of alternative polyadenylation sites
• Gene fusion detection
• Detection of transcript isoforms

Ion AmpliSeq™ Mouse BCR IGH SR Assay, DNA Ion Torrent™

The Ion AmpliSeq Mouse BCR IGH SR Assay, DNA, is a robust, targeted next-generation sequencing (NGS) assay for use in basic and translational immunology, immuno-oncology, hemato-oncology, and vaccine research. It is designed to accurately identify and measure the clonal expansion of B lymphocytes in blood, peripheral blood leukocytes (PBLs), peripheral blood mononuclear cells (PBMCs), and fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples. The assay identifies unique B-cell clones through targeting of the highly diverse complementarity-determining region 3 (CDR3) of the B-cell receptor (BCR) immunoglobulin heavy (IGH) chain from genomic DNA template. The nucleotide sequence of the IGH CDR3 region serves as a natural barcode to enable clone tracking and measurements of B-cell clonal expansion and diversity. Analysis of IGH CDR3-region amino acid motifs may reveal signatures of B-cell responses to defined antigens. For RNA samples, please see Cat. No. A45487.

Benefits of the Ion AmpliSeq Mouse BCR IGH SR Assay, DNA, include:
Compatibility with a vast array of research sample types, including FFPE tissue, fresh-frozen (FF) tissue, whole blood, PBLs, and PBMCs
High sensitivity and low limit of detection (LoD) for rare clone identification through dual-barcode indexing
Efficient workflow with 48 hour sample-to-results time
Flexible input requirements ranging from 100 ng to 2 µg
Streamlined and user-friendly informatics solution with automated clonotyping, clonal lineage analysis, reporting of key repertoire features, and multi-sample analysis capability to enable tracking of B-cell clones across mouse research samples

The Ion AmpliSeq Mouse BCR IGH SR Assay with DNA input uses multiplex PCR primers to generate 90-bp amplicons that can be sequenced on all chip types supported by the Ion GeneStudio S5 sequencing systems, allowing you to pick the best multiplexing configuration for your unique sample batching needs and throughput requirements. The entire workflow, from library preparation to analysis of samples, can be accomplished in two days using the Ion Chef templating system and Ion GeneStudio S5 system. The assay kit provides a single pool of multiplex PCR primers, dNTPs, and library reagents.

The Ion AmpliSeq Mouse BCR IGH SR Assay, DNA, supports key applications in immunology, immuno-oncology, hemato-oncology, and vaccine research. The high-sensitivity dual-barcode indexing, flexible input requirements (100 ng–2 µg), compatibility with degraded materials, and high-throughput capability make this assay ideal for a range of research applications, including investigations into the role of B cells in anti-cancer immune responses to immunotherapies utilizing checkpoint blockade inhibitors, cancer vaccines, and chimeric antigen receptor (CAR) T cells, as well as infectious and autoimmune disease basic research.

Note: Information about data analysis using Ion Reporter Software v5.12 can be found in the User Guide below.

IonCode™ Barcode Adapters 1-384 Kit Ion Torrent™

The IonCode Barcode Adapters 1-384 Kit provides a set of 384 unique barcode adapters specifically designed for optimal performance with the Ion GeneStudio S5, Ion PGM, and Ion Proton semiconductor sequencers. When used in combination with Ion Barcode Adapters 385-768 and Ion AmpliSeq Library Kit PLUS or Ion AmpliSeq Library Kit 2.0, this kit enables users to pool up to 768 amplicon libraries and then conduct multiplexed sequencing analysis, simplifying the Ion semiconductor sequencing workflow for a wide range of applications, including targeted enrichment.

Key product features:

• Enables multiplexing of numerous amplicon library samples on a single sequencing chip with the use of robust molecular barcodes
• Both sequence- and flow-optimized for equal representation of all barcodes in a pool and more economical multiplexed sequencing runs
• Robust error correction built in by design for added confidence in sample identification

Multiplexing with barcode adapters enables higher throughput
Multiplexing with barcoded libraries leads to more cost effective runs by permitting up to 768 samples per run, significantly decreasing the cost and handling requirements of sequencing. Each barcode was individually tested to minimize representation bias.

Sequence- and flow-optimized for increased performance and efficiency
Barcode adapters contain sequences that are optimized to provide equal representation of all barcodes in a pool and require minimal number of flows to interrogate, resulting in more economical multiplexed sequencing runs.

Robust error correction built in by design
Built-in error correction prevents the possibility of incorrect sample assignment.

Collibri™ PCR-free PS DNA Library Prep Kit for Illumina™ Systems with UD indexes (Set A-D, 1-96) Invitrogen™

The Invitrogen Collibri PCR-Free 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 PCR-Free 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 improved coverage of challenging genomic regions compared to already available library prep technologies
• Supports PCR-free protocols starting with as little as 500 ng of DNA
• Provides up to 96 combinatorial dual or unique dual indexes
• Is applicable for automation of library preparation

The Collibri PCR-Free PS DNA Library 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 PCR-Free PS DNA Library Prep Kit offers higher confidence SNP and INDEL calls resulting from stronger coverage of challenging genomic regions from inputs as low as 500 ng of physically sheared double-stranded DNA (see figure below). 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 PS DNA Library Prep Kit is recommended for:
• Whole genome sequencing
• Resequencing
• de novo assembly

Oncomine Lung Cell-Free Total Nucleic Acid Research Assay Ion Torrent™

The Oncomine Lung cfTNA Research Assay is part of a complete solution to detect lung tumor-derived cell-free DNA and RNA (cell-free total nucleic acid; cfTNA) isolated from the plasma fraction of whole blood. It provides the reagents for library construction and a single pool of multiplex PCR primers for preparation of amplicon libraries from cfTNA obtained from the plasma fraction of a single 10 mL tube of whole blood.

Liquid biopsies offer several advantages over conventional solid tumor biopsies:
• Less invasive, enabling them to be taken at multiple time points to monitor progression of the cancer
• Lower cost
• Faster turnaround time from sample to results
• Better represent tumor heterogeneity

The Oncomine Lung cfTNA Research Assay enables the analysis of:
• Hotspot genes (SNVs) and short indels: ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, ROS1, and TP53 (~168 hotspots covered)
• Gene fusions: ALK, RET, ROS1
• MET exon 14 skipping
• Copy number gene (CNV): MET

These genes have been identified as frequently mutated in non-small cell lung cancer (NSCLC). Through the use of Tag Sequencing technology, low limits of detection (LOD) can be achieved for different variant types*:
• For SNVs/short indels, an LOD of 0.1% can be achieved with sensitivity of ~90% and specificity of >99%
• For fusions & MET exon skipping, an LOD of 1% can be achieved with sensitivity of >90% and specificity of >99%
• For MET CNV target, detection as low as 1.2-fold amplification can be achieved with sensitivity of >90% and specificity of >99%

The entire workflow from isolation of cfTNA using the MagMAX Cell-Free Total Nucleic Acid Isolation Kit to analysis of samples can be accomplished in just two days using the Ion S5 XL sequencing system.

Technology
cfDNA and cfRNA are found at extremely low concentrations in the plasma fraction of whole blood. Because of this low prevalence, a tag sequencing technology is utilized in this assay. The technology attaches unique molecular tags to the gene-specific primers (figure below). After amplification, the tagged molecules are grouped based on the tags. Groups containing the same mutant variant 80% of the time or greater will be called positive. Using the Tag technology, groups that contain random errors generated through the library construction/sequencing process are removed.

Unlike other technologies with LODs of 1-5%, the Oncomine Lung cfTNA Research Assay has a flexible detection limit down to 0.1% for SNVs or one mutant copy in a background of 1,000 wild-type copies. To achieve 0.1% LOD, 20 ng of input cfDNA is required. Lower amounts of cfTNA can be used, but the %LOD will be higher depending on the input amount.

Advantages:
• Optimized amplicon design for short cfDNA ensures highest possible capture rate
• Tag Sequencing technology minimizes false positives by removing randomly incorporated errors
• Optimized targeted assay design allows highly multiplexed next-generation sequencing (NGS), reducing
sequencing costs per sample
• Efficient 2-day workflow

Analysis of SNVs and short indels can be achieved using Torrent Suite Software 5.2 or higher. In order to analyze SNVs, short indels, fusion, and CNVs, Ion Reporter 5.6 (cloud- or server-based) is required.

Simplicity, speed, and scalability of TagSequencing technology
The Oncomine Lung cfTNA Research Assay enables cancer genetic studies from just 5 ng of input cfTNA for targeted library construction. The Oncomine Lung cfTNA Research Assay is compatible with FFPE samples for possible concordance studies. Total time to targeted libraries is just four hours. Scalability and flexibility are achieved using the Tag Sequencing Barcode Set 1-24 or 25-48 (Cat. Nos. A31830, A31847) for multiplexing barcoded samples on Ion S5 chips.

*Sensitivity and specificity for each variant type were determined using a collection of contrived positive samples and cfTNA isolated from normal healthy donors.

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™ 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.

Ion AmpliSeq™ Mouse BCR IGH SR Assay, RNA Ion Torrent™

The Ion AmpliSeq Mouse BCR IGH SR Assay, RNA, is a robust, targeted next-generation sequencing (NGS) assay for use in basic and translational immunology, immuno-oncology, hemato–oncology, and vaccine research. It is designed to accurately identify and measure the clonal expansion of B lymphocytes in blood, peripheral blood leukocytes (PBLs), peripheral blood mononuclear cells (PBMCs), and fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples. The assay identifies unique B-cell clones through targeting of the highly diverse complementarity-determining region 3 (CDR3) of the B-cell receptor (BCR) immunoglobulin heavy (IGH) chain from genomic DNA template . The nucleotide sequence of the IGH CDR3 region serves as a natural barcode to enable clone tracking and measurements of B-cell clonal expansion and diversity. Analysis of IGH CDR3-region amino acid motifs may reveal signatures of B-cell responses to defined antigens.

Benefits of the Ion AmpliSeq Mouse BCR IGH SR Assay, RNA, include:
Compatibility with a vast array of research sample types, including FFPE tissue, fresh-frozen (FF) tissue, whole blood, PBLs, and PBMCs
High sensitivity and low limit of detection (LoD) for rare clone identification through dual-barcode indexing
Efficient workflow with 48 hour sample-to-results time
Flexible input requirements ranging from 100 ng to 1 µg
Streamlined and user-friendly informatics solution with with multi-sample analysis functionality

The Ion AmpliSeq Mouse BCR IGH SR Assay, RNA, provides a single pool of multiplex PCR primers and library reagents to generate 90-bp amplicons that can be sequenced on all chip types supported by the Ion GeneStudio S5 sequencing systems, allowing you to pick the best multiplexing configuration for your unique sample batching needs and throughput requirements. The entire workflow, (from library preparation to analysis of samples, can be accomplished in two days using the Ion Chef templating system and Ion GeneStudio S5 system..

The Ion AmpliSeq Mouse BCR IGH SR Assay, RNA, with its high sensitivity and specificity, supports key applications in immunology, immuno-oncology, hemato-oncology, and vaccine research. The high-sensitivity dual-barcode indexing, flexible input requirements (100 ng–1 µg), high-depth sequencing, and high-throughput capability make this assay ideal for testing variety of hypothesis for basic or translational biomarker research. A small fragment-size requirement for the input materials for library creation and high multiplexing on the Ion 530 Chip of the Ion GeneStudio S5 sequencer enables researchers to focus on testing a variety of use cases in mouse models, including the role of T cells in generating immune response to immunotherapies such as checkpoint blockade inhibitors, cancer vaccines, or chimeric antigen receptor (CAR) T-cell therapies.

Note: Information about data analysis using Ion Reporter Software v5.12 can be found in the User Guide below.

Ion AmpliSeq™ Library Kit 2.0 Ion Torrent™

The Ion AmpliSeq™ Library Kit 2.0 is designed for rapid preparation of amplicon libraries using Ion AmpliSeq™ panels.

Scalable Multiplex PCR Reactions
The Ion AmpliSeq 2.0 technology enables scalable multiplex PCR reactions from 12- to 24,000-plex in a single well using just 10 ng of starting DNA. Ion AmpliSeq panels and primer pools allow highly multiplexed PCR amplification of thousands of genomic target regions, with superior coverage uniformity and specificity, without the need of a specialized microfluidics PCR platform. In addition, the primers contain proprietary modifications that enable removal of primer sequences during library preparation, for efficient target assessment during sequencing. Multiple primer pools can be used to create overlapping amplicons that enable complete coverage of large targets. Ion AmpliSeq™ Custom Primer Pools are designed via the Ion AmpliSeq™ Designer Tool, available at www.ampliseq.com.

Barcoded Library Preparation
The Ion AmpliSeq Library Kit 2.0 includes reagents for generating amplicons with 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 allow for accurate sample-to-sample comparisons.

Easy and Flexible Protocol
The Ion AmpliSeq Library Kit 2.0 uses a plate-based format for easier sample handling and tracking, and for compatibility with automation and high-throughput laboratories. The library preparation uses very small quantities of starting material per PCR. The resulting DNA 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.

Ion PI™ Chip Kit v3 Ion Torrent™

The Ion PI™ Chip Kit v3 contains 8 barcoded chips for sample tracking and sequencing with the Ion Proton™ System. The Ion PI™ Chip electronically detects polymerase-driven base incorporation without the use of fluorescence. By eliminating the use of an optical detection system, this revolutionary advance in next-generation sequencing technology allows for rapid sequencing times of less than 4 hours. The Ion PI™ Chip v3 enables a simplified sequencing workflow with the removal of chip preparation steps, reducing the hands-on time by approximately 45 minutes compared to previous versions.

The Ion PI™ Chip Kit v3 offers:
• A simplified workflow, reducing hands-on time by approximately 45 minutes
• Barcoded sequencing chip with sample tracking functionality
• 10 Gb of sequence data with a rapid run time of typically only 2-4 hours
• Support for a variety of applications, including sequencing of up to three human exomes, transcriptome profiling with 60-80 million reads, and targeted resequencing of gene panels

Notes
This kit is only compatible with the Ion Proton™ System.
Use this kit with the Ion PI™ Hi-Q OT2 200 Kit and Ion PI™ Hi-Q Sequencing 200 Kit.
This kit replaces the Ion PI™ Chip Kit v2 & Ion PI™ Chip Kit v2 BC.
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