White Papers

Biomarker Discovery & Validation

Infrared detection decreases nitrocellulose autofluorescence and improves RPPA assays signal‐to‐noise ratio over visible wavelength detection

Protein array applications in disease biomarker discovery and validation reflect the enormous potential of protein arrays in the field of personalized medicine. Until now, the rise of protein array technology was limited by high fluorescence emitted by nitrocellulose. The InnoScan 710-IR infrared microarray scanner now allows an increased signal-to-noise ratio and thus sensitivity of RPPAs by decreasing background fluorescence. In addition, with a high resolution of up to 3 µm per pixel, it allows the acquisition of high quality images.

Tools & Technology
,
Microarrays & Multiplexing
,
Research & Discovery
,
Proteomics & Protein Research
,
Biomarker Discovery & Validation

Reducing the variability of pre-analytical handling of biological samples

The increasing use of biomarkers as diagnostic indicators of pathological conditions, as monitors of disease progression or as surrogate markers of patient outcomes in clinical trials has led to a huge increase in the number of biological samples whose accurate analysis is of vital importance...

Tools & Technology
,
Sample Prep
,
Clinical & Translational
,
Biomarker Discovery & Validation

Cancer

Caris Life Sciences rapidly deploys IBM high-performance computing solution

As the molecular profiling Caris Life Sciences performs for cancer patients has advanced, the company's needs for managing high-performance analytics and storage have grown exponentially. Its next-generation sequencing (NGS) processes are now fully supported by IBM supercomputing technologies, including processing by IBM NeXtScale System servers.

Tools & Technology
,
Informatics
,
Sequencing Technology
,
Cancer

Cell Biology Research

Production of Large Quantities of Mouse and Rabbit Monoclonal Antibodies using the FiberCell Systems Inc. Bioreactor

The FiberCell Systems hollow fiber bioreactor allows the production of about 50 - 200 mg of antibody per month from standard hybridomas using the small/medium sized reactor. The advantage of this system is that antibody production can be performed in chemically defined media (no proteins at all) resulting in pure hydridoma generated antibody with no antibody contamination from fetal bovine serum or mouse ascities. The product also is harvested in a concentrated form 500 3000 μ/ml and production of the antibody can be accomplished in a standard CO2 incubator.

Cell Biology Research
,
Research & Discovery

In Vitro Toxicology and Hollow Fiber Bioreactors

The recent introduction of hollow fiber bioreactor cartridges represents an important advancement in the field of in vitro toxicology. Most toxicologists believe in vitro testing methods are a useful, time and cost effective tool for drug discovery but it is generally accepted that many of the available tests are not effective for examining both time and concentration, and do not closely mimic human kinetics. This is because they do not properly take into account pharmacodynamic actions (what a drug does to the body) and pharmacokinetic actions (what a body does to the drug). Recently, with the use of hollow fiber bioreactor cartridges, this has changed.

Cell Biology Research
,
Research & Discovery

Continuous Collection of Stem Cells from a Human Placenta Perfusion Co-Culture

The human placenta represents an attractive source of stem cells as it is readily available, provides large numbers of cells and presents low ethical constraints. The potential for human placenta-derived cells to produce stem cells in a hollow fiber bioreactor co-culture system was investigated.

Research & Discovery
,
Cell Biology Research

Production of Recombinant Proteins and Monoclonal Antibodies in Hollow Fiber Bioreactors

The production of secreted products from mammalian cells such as recombinant proteins and monoclonal antibodies is generally performed in standard flask, roller or spinner culture. The typical cycle of seeding cells at a very low density in an excess of medium and then harvesting (often quite aggressively) just before the point of medium exhaustion, is itself a very unnatural system. It is only recently understood how dramatically culture conditions can affect protein quality.

Research & Discovery
,
Cell Biology Research

Clinical & Translational

Reducing the variability of pre-analytical handling of biological samples

The increasing use of biomarkers as diagnostic indicators of pathological conditions, as monitors of disease progression or as surrogate markers of patient outcomes in clinical trials has led to a huge increase in the number of biological samples whose accurate analysis is of vital importance...

Tools & Technology
,
Sample Prep
,
Clinical & Translational
,
Biomarker Discovery & Validation

Clinical Sequencing

IBM Platform Computing Cloud Service for BIOVIA NGS Workflow

This document describes the reference architecture for the IBM Platform Computing Cloud Service for BIOVIA NGS Workflow, which is a public cloud based technical computing architecture that supports the BIOVIA NGS Workflow. The IBM Platform Computing Cloud Service brings to market high performance compute capability that is crafted in IBM SoftLayer public cloud data centers across the globe. A powerful combination of IBM Platform Computing software and SoftLayer cloud infrastructure.

Tools & Technology
,
Informatics
,
Sequencing Technology
,
Clinical Sequencing

Gene Expression Research

Lower Cost, Higher Throughput Library Preparation with the Echo Liquid Handler and the NuGEN Ovation Single Cell RNA-Seq System

In this proof of concept study (POC), the Ovation Single Cell RNA-Seq System miniaturization was validated by examining libraries prepared and sequenced at traditional and miniaturized reaction volumes. Additionally, the sample and reagent transfers were automated using the Echo acoustic liquid handling technology. Echo liquid handlers transfer a wide range of fluids without contact of tips or recalibration between fluid types. The industry leading accuracy and precision of Echo liquid handlers at microliter and nanoliter volumes in combination with the NuGEN Ovation Single Cell RNA-Seq System increases library preparation throughput while reducing the costs. This enables a broader application of transcriptome analysis with NGS.

Tools & Technology
,
PCR
,
Research & Discovery
,
Gene Expression Research

High Throughput RT-qPCR for Gene Expression Analysis

The current standard of accuracy for quantification of gene expression is reverse transcriptase quantitative PCR (RT-qPCR). A new, cost-effective sample preparation method for RT-PCR incorporates a “one-step” cell lysis buffer which eliminates the need for mRNA isolation and purification. This improved method, when combined with nanoscale non-contact liquid handling technology enables a high throughput automated workflow for gene expression.

Tools & Technology
,
PCR
,
Gene Expression Research

Automated RT-qPCR Utilizing the Access Workstation, the Echo Liquid Handler, and RealTime Ready Reagents from Roche Applied Science

RT-qPCR has been increasingly utilized by researchers to quantify mRNA levels. Its widespread use has been limited by an often laborious multi-step process and high reagent cost. Recent advances in non-contact reagent dispensing and next generation one step lysis reagents are enabling scientists to generate high throughput data at a much faster rate. This technical note describes the automation of three complementary tools to generate high throughout RT-qPCR data; the Echo liquid handler, RealTime Ready cell lysis reagents, and the Access workstation.

Tools & Technology
,
PCR
,
Gene Expression Research

Informatics

Caris Life Sciences rapidly deploys IBM high-performance computing solution

As the molecular profiling Caris Life Sciences performs for cancer patients has advanced, the company's needs for managing high-performance analytics and storage have grown exponentially. Its next-generation sequencing (NGS) processes are now fully supported by IBM supercomputing technologies, including processing by IBM NeXtScale System servers.

Tools & Technology
,
Informatics
,
Sequencing Technology
,
Cancer

Accelerating Life Sciences Research

Hadoop MapReduce is fast becoming a core technology in the exciting fast moving field of genome research. This whitepaper explains how IBM Platform Symphony helps dramatically accelerate Contrail, an important toolset in de novo genome assembly.

Tools & Technology
,
Informatics
,
Sequencing Technology

IBM Platform Computing Cloud Service for CLC Bio

This document describes the reference architecture for the IBM Platform Computing Cloud Service for CLC bio, which is a public cloud based technical computing architecture that supports the CLC Genomics Server. The IBM Platform Computing Cloud Service brings to market high performance compute capability crafted in IBM SoftLayer public cloud data centers across the globe. A powerful combination of IBM Platform Computing software and SoftLayer cloud infrastructure.

Tools & Technology
,
Informatics
,
Sequencing Technology

IBM Platform Computing Cloud Service for BIOVIA NGS Workflow

This document describes the reference architecture for the IBM Platform Computing Cloud Service for BIOVIA NGS Workflow, which is a public cloud based technical computing architecture that supports the BIOVIA NGS Workflow. The IBM Platform Computing Cloud Service brings to market high performance compute capability that is crafted in IBM SoftLayer public cloud data centers across the globe. A powerful combination of IBM Platform Computing software and SoftLayer cloud infrastructure.

Tools & Technology
,
Informatics
,
Sequencing Technology
,
Clinical Sequencing

Advancing Bioinformatics with Platform Symphony Advanced Edition

IBM Platform Symphony enables greater resource utilization and performance gain within the genomic data science center. It also examines the deployment and management of bioinformatics compute models that leverage MapReduce in both public and private clouds.

Tools & Technology
,
Informatics
,
Sequencing Technology

Speed, SCALE, SMARTS - IBM reference architecture for genomics brings power to research

Reprint of article by Frank Lee, first published in IBM Systems Magazine. IBM, in collaboration with key researchers and partners, created the IBM reference architecture for genomics. The end-to-end reference architecture defines the enterprise data management, workflow orchestration and global access capabilities across key genomics, translational and personalized medicine platforms. It supports large-scale genomics sequencing and downstream data analytics, providing: data lifecycle management to support large scale data growth; software-based abstraction layers for compute, storage, big data and cloud; and workload and workflow orchestrator for applications.

Tools & Technology
,
Informatics
,
Sequencing Technology

LIMS: Four Reasons Buying is Better than Building

Has your lab come to the realization that you need a LIMS but can't decide whether to buy one or build one internally? Before you make a decision, read this white paper. In it, we describe why several preeminent labs made the decision to buy instead of build.

Tools & Technology
,
Informatics
,
Sequencing Technology

Conducting Clinical Next-Generation Sequencing: How to Manage Change, CLIA, NGS and Informatics

The drive toward personalized medicine has led many labs to consider conducting clinical tests employing next-generation sequencing, but the decision to do so requires labs to consider how they will conduct this work under the auspices of CLIA or CAP requirements. This paper outlines the general principles of CLIA certification and its specific application to clinical NGS, from the perspective of both research and clinical labs.

Tools & Technology
,
Informatics
,
Sequencing Technology

Reading the Writing on the Wall: Four Telltale Signs That You Might Need a LIMS

Many labs shy away from the notion of upgrading to a laboratory information management system because they are happy with spreadsheets, but if your lab is expanding, processing new samples, or offering new services, you may need to upgrade to a more formal or structured solution. This paper poses four questions for labs to determine if it's time to make the leap to a LIMS.

Tools & Technology
,
Informatics

Taking NAS to the Cloud

The flood of genomic (and other life sciences) data has just begun. A central challenge for large and small organizations generating the massive data treasure trove is how to store and manage the data. This article discusses leveraging cloud storage for data deluge in the sciences.

Tools & Technology
,
Informatics

Life Science Storage & Data Management Guide

This white paper will distill many of observed storage and NGS data management related issues as well as the current expert perspective on the life science storage, NGS and data management landscape.

Tools & Technology
,
Informatics

Microarrays & Multiplexing

Reverse Phase Protein Arrays for Cell Signaling: Using the InnoScan 710-IR scanner improves sensitivity and dynamic range.

Reverse Phase Protein Arrays (RPPAs) are increasingly used to study cell signaling as they are highly multiplexed and allow precise quantification of protein of interests in biological samples. Such arrays promote automation, simplified work flow, and preserve sample.  One of the principal challenges faced by RPPAs is to find the best combination of an array surface that will support high binding levels of viable protein probes, and a detection method that will provide high sensitivity and dynamic range. With the new InnoScan 710-IR scanner it is now possible to combine infrared detection with high sensitivity and quality images.

Tools & Technology
,
Microarrays & Multiplexing
,
Research & Discovery
,
Proteomics & Protein Research

Infrared detection decreases nitrocellulose autofluorescence and improves RPPA assays signal‐to‐noise ratio over visible wavelength detection

Protein array applications in disease biomarker discovery and validation reflect the enormous potential of protein arrays in the field of personalized medicine. Until now, the rise of protein array technology was limited by high fluorescence emitted by nitrocellulose. The InnoScan 710-IR infrared microarray scanner now allows an increased signal-to-noise ratio and thus sensitivity of RPPAs by decreasing background fluorescence. In addition, with a high resolution of up to 3 µm per pixel, it allows the acquisition of high quality images.

Tools & Technology
,
Microarrays & Multiplexing
,
Research & Discovery
,
Proteomics & Protein Research
,
Biomarker Discovery & Validation

miRNA/RNAi

RNAi Screening in Primary Cells

Screening approaches involving either overexpression or RNAi-mediated down-regulation of genes have become a potent tool for identifying drug targets. Such screens require transfection of cells with e.g. cDNA or shRNA vectors or siRNA oligonucleotides. One important factor for screening success is the ability to efficiently transfect biologically relevant cells. Lonza’s Nucleofector Technology is a proven non-viral method for efficient transfection of primary cells, e.g. human T cells. The HT Nucleofector System, a 384-well platform, expands its application range to high-throughput transfections. With its fast plate processing time and easy integration into liquid handling systems it is a convenient tool for siRNA, shRNA or miRNA screens in biologically relevant cell types. 

miRNA/RNAi
,
Tools & Technology

Miniaturizing siRNA Transfection Using the Echo Liquid Handler

Large-scale, high-throughput siRNA experiments require a transfer system that can facilitate reliable and reproducible transfections in high-density well-plate formats, as well as effective delivery of the siRNA molecule. This study demonstrates superior performance of the Echo liquid handler compared to more traditional liquid handling methods for standard, reverse and lipid-free transfection of siRNA molecules into mammalian cells. Results of the study clearly demonstrate the ability of the Echo liquid handler to deliver comparable transfection efficiency, knock-down and cell morphology to reactions prepared using traditional pipeting methods. In fact, reactions prepared with the Echo liquid handler were miniaturized to use significantly less volume of siRNA and other reagents, and still yielded more representative inclusion intensities than traditional manual pipetting techniques. Such miniaturization can result in significant cost savings and greater confidence in the results from siRNA screening studies.

Tools & Technology
,
miRNA/RNAi

PCR

Miniaturization of DNA Assembly for Synthetic Biology

Traditional DNA assembly methods require reactions of 10-20 microliters per well. The Echo liquid handler can reduce that volume 10-fold, drastically cutting costs. With the ability to reliably transfer volumes as low as 2.5 nanoliters, Echo systems can extend the useful life of a primer library and eliminate the need to dilute high concentration primers, saving on storage and primer costs, and preventing dilution errors. 

Tools & Technology
,
PCR

Lower Cost, Higher Throughput Library Preparation with the Echo Liquid Handler and the NuGEN Ovation Single Cell RNA-Seq System

In this proof of concept study (POC), the Ovation Single Cell RNA-Seq System miniaturization was validated by examining libraries prepared and sequenced at traditional and miniaturized reaction volumes. Additionally, the sample and reagent transfers were automated using the Echo acoustic liquid handling technology. Echo liquid handlers transfer a wide range of fluids without contact of tips or recalibration between fluid types. The industry leading accuracy and precision of Echo liquid handlers at microliter and nanoliter volumes in combination with the NuGEN Ovation Single Cell RNA-Seq System increases library preparation throughput while reducing the costs. This enables a broader application of transcriptome analysis with NGS.

Tools & Technology
,
PCR
,
Research & Discovery
,
Gene Expression Research

Automated RT-qPCR Utilizing the Access Workstation, the Echo Liquid Handler, and RealTime Ready Reagents from Roche Applied Science

RT-qPCR has been increasingly utilized by researchers to quantify mRNA levels. Its widespread use has been limited by an often laborious multi-step process and high reagent cost. Recent advances in non-contact reagent dispensing and next generation one step lysis reagents are enabling scientists to generate high throughput data at a much faster rate. This technical note describes the automation of three complementary tools to generate high throughout RT-qPCR data; the Echo liquid handler, RealTime Ready cell lysis reagents, and the Access workstation.

Tools & Technology
,
PCR
,
Gene Expression Research

High Throughput RT-qPCR for Gene Expression Analysis

The current standard of accuracy for quantification of gene expression is reverse transcriptase quantitative PCR (RT-qPCR). A new, cost-effective sample preparation method for RT-PCR incorporates a “one-step” cell lysis buffer which eliminates the need for mRNA isolation and purification. This improved method, when combined with nanoscale non-contact liquid handling technology enables a high throughput automated workflow for gene expression.

Tools & Technology
,
PCR
,
Gene Expression Research

High-throughput Miniaturized Quantitative PCR with the Echo 525 Liquid Handler

Quantitative PCR (qPCR) is a prevalent tool spanning many phases of drug discovery. Advances in qPCR detection to enable 384- and 1536-well microplate formats have incentivized researchers to miniaturize qPCR assays as a means to offset the costs of increasing throughput. To significantly reduce qPCR volumes and maintain data quality, the liquid handling methods employed for such low-volume transfers must be precise and accurate. Tipless, touchless acoustic droplet ejection with the Echo liquid handler eliminates the cost of disposable tips or tip-wash cycles and simplifies assay setup by eliminating dilution steps. This study utilized the Echo 525 liquid handler to assemble low-volume qPCR assays at speeds that keep pace with high-throughput demands. The results demonstrated the Echo 525 liquid handler effectively miniaturized reaction volumes for high-throughput qPCR in both 384- and 1536-well formats.

Tools & Technology
,
PCR

Proteomics & Protein Research

Infrared detection decreases nitrocellulose autofluorescence and improves RPPA assays signal‐to‐noise ratio over visible wavelength detection

Protein array applications in disease biomarker discovery and validation reflect the enormous potential of protein arrays in the field of personalized medicine. Until now, the rise of protein array technology was limited by high fluorescence emitted by nitrocellulose. The InnoScan 710-IR infrared microarray scanner now allows an increased signal-to-noise ratio and thus sensitivity of RPPAs by decreasing background fluorescence. In addition, with a high resolution of up to 3 µm per pixel, it allows the acquisition of high quality images.

Tools & Technology
,
Microarrays & Multiplexing
,
Research & Discovery
,
Proteomics & Protein Research
,
Biomarker Discovery & Validation

Reverse Phase Protein Arrays for Cell Signaling: Using the InnoScan 710-IR scanner improves sensitivity and dynamic range.

Reverse Phase Protein Arrays (RPPAs) are increasingly used to study cell signaling as they are highly multiplexed and allow precise quantification of protein of interests in biological samples. Such arrays promote automation, simplified work flow, and preserve sample.  One of the principal challenges faced by RPPAs is to find the best combination of an array surface that will support high binding levels of viable protein probes, and a detection method that will provide high sensitivity and dynamic range. With the new InnoScan 710-IR scanner it is now possible to combine infrared detection with high sensitivity and quality images.

Tools & Technology
,
Microarrays & Multiplexing
,
Research & Discovery
,
Proteomics & Protein Research

Research & Discovery

Lower Cost, Higher Throughput Library Preparation with the Echo Liquid Handler and the NuGEN Ovation Single Cell RNA-Seq System

In this proof of concept study (POC), the Ovation Single Cell RNA-Seq System miniaturization was validated by examining libraries prepared and sequenced at traditional and miniaturized reaction volumes. Additionally, the sample and reagent transfers were automated using the Echo acoustic liquid handling technology. Echo liquid handlers transfer a wide range of fluids without contact of tips or recalibration between fluid types. The industry leading accuracy and precision of Echo liquid handlers at microliter and nanoliter volumes in combination with the NuGEN Ovation Single Cell RNA-Seq System increases library preparation throughput while reducing the costs. This enables a broader application of transcriptome analysis with NGS.

Tools & Technology
,
PCR
,
Research & Discovery
,
Gene Expression Research

Infrared detection decreases nitrocellulose autofluorescence and improves RPPA assays signal‐to‐noise ratio over visible wavelength detection

Protein array applications in disease biomarker discovery and validation reflect the enormous potential of protein arrays in the field of personalized medicine. Until now, the rise of protein array technology was limited by high fluorescence emitted by nitrocellulose. The InnoScan 710-IR infrared microarray scanner now allows an increased signal-to-noise ratio and thus sensitivity of RPPAs by decreasing background fluorescence. In addition, with a high resolution of up to 3 µm per pixel, it allows the acquisition of high quality images.

Tools & Technology
,
Microarrays & Multiplexing
,
Research & Discovery
,
Proteomics & Protein Research
,
Biomarker Discovery & Validation

Assessing Quality Using ACCURUN Controls for Quantitative Viral Load Assays

ACCURUN controls from SeraCare Life Sciences are developed and manufactured as third-party controls. These products are designed to support the quality control procedures within clinical labs. When used properly and as part of an overall QC program, ACCURUN controls will monitor assay accuracy and precision, help identify performance issues and improve the work efficiency of a clinical lab. The ultimate goal of the QC program is to provide added confidence in the reliability and validity of the reported results.

Tools & Technology
,
Research & Discovery

Reverse Phase Protein Arrays for Cell Signaling: Using the InnoScan 710-IR scanner improves sensitivity and dynamic range.

Reverse Phase Protein Arrays (RPPAs) are increasingly used to study cell signaling as they are highly multiplexed and allow precise quantification of protein of interests in biological samples. Such arrays promote automation, simplified work flow, and preserve sample.  One of the principal challenges faced by RPPAs is to find the best combination of an array surface that will support high binding levels of viable protein probes, and a detection method that will provide high sensitivity and dynamic range. With the new InnoScan 710-IR scanner it is now possible to combine infrared detection with high sensitivity and quality images.

Tools & Technology
,
Microarrays & Multiplexing
,
Research & Discovery
,
Proteomics & Protein Research

Production of Large Quantities of Mouse and Rabbit Monoclonal Antibodies using the FiberCell Systems Inc. Bioreactor

The FiberCell Systems hollow fiber bioreactor allows the production of about 50 - 200 mg of antibody per month from standard hybridomas using the small/medium sized reactor. The advantage of this system is that antibody production can be performed in chemically defined media (no proteins at all) resulting in pure hydridoma generated antibody with no antibody contamination from fetal bovine serum or mouse ascities. The product also is harvested in a concentrated form 500 3000 μ/ml and production of the antibody can be accomplished in a standard CO2 incubator.

Cell Biology Research
,
Research & Discovery

In Vitro Toxicology and Hollow Fiber Bioreactors

The recent introduction of hollow fiber bioreactor cartridges represents an important advancement in the field of in vitro toxicology. Most toxicologists believe in vitro testing methods are a useful, time and cost effective tool for drug discovery but it is generally accepted that many of the available tests are not effective for examining both time and concentration, and do not closely mimic human kinetics. This is because they do not properly take into account pharmacodynamic actions (what a drug does to the body) and pharmacokinetic actions (what a body does to the drug). Recently, with the use of hollow fiber bioreactor cartridges, this has changed.

Cell Biology Research
,
Research & Discovery

Continuous Collection of Stem Cells from a Human Placenta Perfusion Co-Culture

The human placenta represents an attractive source of stem cells as it is readily available, provides large numbers of cells and presents low ethical constraints. The potential for human placenta-derived cells to produce stem cells in a hollow fiber bioreactor co-culture system was investigated.

Research & Discovery
,
Cell Biology Research

Production of Recombinant Proteins and Monoclonal Antibodies in Hollow Fiber Bioreactors

The production of secreted products from mammalian cells such as recombinant proteins and monoclonal antibodies is generally performed in standard flask, roller or spinner culture. The typical cycle of seeding cells at a very low density in an excess of medium and then harvesting (often quite aggressively) just before the point of medium exhaustion, is itself a very unnatural system. It is only recently understood how dramatically culture conditions can affect protein quality.

Research & Discovery
,
Cell Biology Research

Sample Prep

Precise Sizing and SMRT Sequencing Offer Unprecedented Read Length for Clinical Studies

Using BluePippin significantly extends average read length for PacBio. Read this case study to learn how Robert Sebra at the Icahn Institute for Genomics and Multiscale Biology uses automated DNA size selection to maximize read length with SMRT Sequencing.

Tools & Technology
,
Sequencing Technology
,
Sample Prep

Miniaturization of Multiple Displacement Amplification of Genomes from a Single Cell

Advances in whole-genome amplification have enabled sequencing of DNA and RNA from a single cell, or what is commonly called Single-cell Genomics (SGC). Despite the growing interest in SGC, a standardized method for sample preparation currently does not exist. However in a recent Nature Protocols article, "Obtaining genomes from uncultivated environmental microorganisms using FACS-based single cell genomics," researchers at the Department of Energy Joint Genome Institute describe an approach that can meet the throughput and sample quality required for robust whole-genome amplification from a single cell. This application highlight describes the role of the Echo liquid handler in this new approach. 

Tools & Technology
,
Sample Prep

Scientists Use Pippin to Optimize Nextera Libraries

Learn how Pippin Prep can optimize your Nextera libraries In this case study, Zach Herbert at the Dana-Farber Cancer Institute describes adding automated DNA sizing from Sage Science to his Nextera workflow for better sequence results.

Sequencing Technology
,
Tools & Technology
,
Sample Prep

Reducing the variability of pre-analytical handling of biological samples

The increasing use of biomarkers as diagnostic indicators of pathological conditions, as monitors of disease progression or as surrogate markers of patient outcomes in clinical trials has led to a huge increase in the number of biological samples whose accurate analysis is of vital importance...

Tools & Technology
,
Sample Prep
,
Clinical & Translational
,
Biomarker Discovery & Validation

Technical Note: A New Method of Snap Freezing Bacteria Using BioCision’s CoolRack System

The preservation of bacterial cultures by freezing has long been reported (1,2). Several protocols (3,4) recommend snap freezing in glycerol or DMSO prior to storage. One common way to snap freeze is by submerging samples in a slurry of dry ice and ethanol until frozen. BioCision’s CoolRack module...

Sample Prep

Randomized Adapters for Reducing Bias in Small RNA-Seq Libraries

While next-generation sequencing is the most practical method for identifying small RNAs, bias can skew the resulting data. Bioo Scientific has developed its NEXTflex Small RNA Sequencing Kit v2 to reduce this bias by incorporating a randomized adapter strategy that involves incorporating pools of adapters with randomized bases at critical positions adjacent to the ligation junctions. This application note details a validation study that demonstrates the reduced bias when using a randomized adapter strategy.  

Tools & Technology
,
Sequencing Technology
,
Sample Prep

Sequencing Technology

Accelerating Life Sciences Research

Hadoop MapReduce is fast becoming a core technology in the exciting fast moving field of genome research. This whitepaper explains how IBM Platform Symphony helps dramatically accelerate Contrail, an important toolset in de novo genome assembly.

Tools & Technology
,
Informatics
,
Sequencing Technology

Caris Life Sciences rapidly deploys IBM high-performance computing solution

As the molecular profiling Caris Life Sciences performs for cancer patients has advanced, the company's needs for managing high-performance analytics and storage have grown exponentially. Its next-generation sequencing (NGS) processes are now fully supported by IBM supercomputing technologies, including processing by IBM NeXtScale System servers.

Tools & Technology
,
Informatics
,
Sequencing Technology
,
Cancer

IBM Platform Computing Cloud Service for CLC Bio

This document describes the reference architecture for the IBM Platform Computing Cloud Service for CLC bio, which is a public cloud based technical computing architecture that supports the CLC Genomics Server. The IBM Platform Computing Cloud Service brings to market high performance compute capability crafted in IBM SoftLayer public cloud data centers across the globe. A powerful combination of IBM Platform Computing software and SoftLayer cloud infrastructure.

Tools & Technology
,
Informatics
,
Sequencing Technology

IBM Platform Computing Cloud Service for BIOVIA NGS Workflow

This document describes the reference architecture for the IBM Platform Computing Cloud Service for BIOVIA NGS Workflow, which is a public cloud based technical computing architecture that supports the BIOVIA NGS Workflow. The IBM Platform Computing Cloud Service brings to market high performance compute capability that is crafted in IBM SoftLayer public cloud data centers across the globe. A powerful combination of IBM Platform Computing software and SoftLayer cloud infrastructure.

Tools & Technology
,
Informatics
,
Sequencing Technology
,
Clinical Sequencing

Advancing Bioinformatics with Platform Symphony Advanced Edition

IBM Platform Symphony enables greater resource utilization and performance gain within the genomic data science center. It also examines the deployment and management of bioinformatics compute models that leverage MapReduce in both public and private clouds.

Tools & Technology
,
Informatics
,
Sequencing Technology

Speed, SCALE, SMARTS - IBM reference architecture for genomics brings power to research

Reprint of article by Frank Lee, first published in IBM Systems Magazine. IBM, in collaboration with key researchers and partners, created the IBM reference architecture for genomics. The end-to-end reference architecture defines the enterprise data management, workflow orchestration and global access capabilities across key genomics, translational and personalized medicine platforms. It supports large-scale genomics sequencing and downstream data analytics, providing: data lifecycle management to support large scale data growth; software-based abstraction layers for compute, storage, big data and cloud; and workload and workflow orchestrator for applications.

Tools & Technology
,
Informatics
,
Sequencing Technology

Approaching Single-Cell Sequencing by Understanding NGS Library Complexity and Bias

Next Generation Sequencing (NGS) library bias and library complexity profoundly affect data quality. This application note describes the sequence coverage and preservation of molecular complexity of human and microbial NGS libraries using the Accel-NGS 2S DNA Library Kit. This technology demonstrated 50% higher library complexity and covered 88% of high GC-containing promoter regions better than the market-leading kit.

Tools & Technology
,
Sequencing Technology

LIMS: Four Reasons Buying is Better than Building

Has your lab come to the realization that you need a LIMS but can't decide whether to buy one or build one internally? Before you make a decision, read this white paper. In it, we describe why several preeminent labs made the decision to buy instead of build.

Tools & Technology
,
Informatics
,
Sequencing Technology

Precise Sizing and SMRT Sequencing Offer Unprecedented Read Length for Clinical Studies

Using BluePippin significantly extends average read length for PacBio. Read this case study to learn how Robert Sebra at the Icahn Institute for Genomics and Multiscale Biology uses automated DNA size selection to maximize read length with SMRT Sequencing.

Tools & Technology
,
Sequencing Technology
,
Sample Prep

Conducting Clinical Next-Generation Sequencing: How to Manage Change, CLIA, NGS and Informatics

The drive toward personalized medicine has led many labs to consider conducting clinical tests employing next-generation sequencing, but the decision to do so requires labs to consider how they will conduct this work under the auspices of CLIA or CAP requirements. This paper outlines the general principles of CLIA certification and its specific application to clinical NGS, from the perspective of both research and clinical labs.

Tools & Technology
,
Informatics
,
Sequencing Technology

Increase User Adoption Rates and Realize a Higher Rate of Return on your LIMS Investment

Usability is the key to ensuring that LIMS are adopted and used, but many LIMS developers forget about the end user. This paper describes the traditional barriers to LIMS adoption and explains how these hurdles can be overcome by a focus on usability.

Tools & Technology
,
Sequencing Technology

Scientists Use Pippin to Optimize Nextera Libraries

Learn how Pippin Prep can optimize your Nextera libraries In this case study, Zach Herbert at the Dana-Farber Cancer Institute describes adding automated DNA sizing from Sage Science to his Nextera workflow for better sequence results.

Sequencing Technology
,
Tools & Technology
,
Sample Prep

Randomized Adapters for Reducing Bias in Small RNA-Seq Libraries

While next-generation sequencing is the most practical method for identifying small RNAs, bias can skew the resulting data. Bioo Scientific has developed its NEXTflex Small RNA Sequencing Kit v2 to reduce this bias by incorporating a randomized adapter strategy that involves incorporating pools of adapters with randomized bases at critical positions adjacent to the ligation junctions. This application note details a validation study that demonstrates the reduced bias when using a randomized adapter strategy.  

Tools & Technology
,
Sequencing Technology
,
Sample Prep

Tools & Technology

Accelerating Life Sciences Research

Hadoop MapReduce is fast becoming a core technology in the exciting fast moving field of genome research. This whitepaper explains how IBM Platform Symphony helps dramatically accelerate Contrail, an important toolset in de novo genome assembly.

Tools & Technology
,
Informatics
,
Sequencing Technology

Caris Life Sciences rapidly deploys IBM high-performance computing solution

As the molecular profiling Caris Life Sciences performs for cancer patients has advanced, the company's needs for managing high-performance analytics and storage have grown exponentially. Its next-generation sequencing (NGS) processes are now fully supported by IBM supercomputing technologies, including processing by IBM NeXtScale System servers.

Tools & Technology
,
Informatics
,
Sequencing Technology
,
Cancer

IBM Platform Computing Cloud Service for CLC Bio

This document describes the reference architecture for the IBM Platform Computing Cloud Service for CLC bio, which is a public cloud based technical computing architecture that supports the CLC Genomics Server. The IBM Platform Computing Cloud Service brings to market high performance compute capability crafted in IBM SoftLayer public cloud data centers across the globe. A powerful combination of IBM Platform Computing software and SoftLayer cloud infrastructure.

Tools & Technology
,
Informatics
,
Sequencing Technology

Advancing Bioinformatics with Platform Symphony Advanced Edition

IBM Platform Symphony enables greater resource utilization and performance gain within the genomic data science center. It also examines the deployment and management of bioinformatics compute models that leverage MapReduce in both public and private clouds.

Tools & Technology
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Informatics
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Sequencing Technology

IBM Platform Computing Cloud Service for BIOVIA NGS Workflow

This document describes the reference architecture for the IBM Platform Computing Cloud Service for BIOVIA NGS Workflow, which is a public cloud based technical computing architecture that supports the BIOVIA NGS Workflow. The IBM Platform Computing Cloud Service brings to market high performance compute capability that is crafted in IBM SoftLayer public cloud data centers across the globe. A powerful combination of IBM Platform Computing software and SoftLayer cloud infrastructure.

Tools & Technology
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Informatics
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Sequencing Technology
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Clinical Sequencing

Speed, SCALE, SMARTS - IBM reference architecture for genomics brings power to research

Reprint of article by Frank Lee, first published in IBM Systems Magazine. IBM, in collaboration with key researchers and partners, created the IBM reference architecture for genomics. The end-to-end reference architecture defines the enterprise data management, workflow orchestration and global access capabilities across key genomics, translational and personalized medicine platforms. It supports large-scale genomics sequencing and downstream data analytics, providing: data lifecycle management to support large scale data growth; software-based abstraction layers for compute, storage, big data and cloud; and workload and workflow orchestrator for applications.

Tools & Technology
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Informatics
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Sequencing Technology

Approaching Single-Cell Sequencing by Understanding NGS Library Complexity and Bias

Next Generation Sequencing (NGS) library bias and library complexity profoundly affect data quality. This application note describes the sequence coverage and preservation of molecular complexity of human and microbial NGS libraries using the Accel-NGS 2S DNA Library Kit. This technology demonstrated 50% higher library complexity and covered 88% of high GC-containing promoter regions better than the market-leading kit.

Tools & Technology
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Sequencing Technology

LIMS: Four Reasons Buying is Better than Building

Has your lab come to the realization that you need a LIMS but can't decide whether to buy one or build one internally? Before you make a decision, read this white paper. In it, we describe why several preeminent labs made the decision to buy instead of build.

Tools & Technology
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Informatics
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Sequencing Technology

Miniaturization of DNA Assembly for Synthetic Biology

Traditional DNA assembly methods require reactions of 10-20 microliters per well. The Echo liquid handler can reduce that volume 10-fold, drastically cutting costs. With the ability to reliably transfer volumes as low as 2.5 nanoliters, Echo systems can extend the useful life of a primer library and eliminate the need to dilute high concentration primers, saving on storage and primer costs, and preventing dilution errors. 

Tools & Technology
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PCR

Lower Cost, Higher Throughput Library Preparation with the Echo Liquid Handler and the NuGEN Ovation Single Cell RNA-Seq System

In this proof of concept study (POC), the Ovation Single Cell RNA-Seq System miniaturization was validated by examining libraries prepared and sequenced at traditional and miniaturized reaction volumes. Additionally, the sample and reagent transfers were automated using the Echo acoustic liquid handling technology. Echo liquid handlers transfer a wide range of fluids without contact of tips or recalibration between fluid types. The industry leading accuracy and precision of Echo liquid handlers at microliter and nanoliter volumes in combination with the NuGEN Ovation Single Cell RNA-Seq System increases library preparation throughput while reducing the costs. This enables a broader application of transcriptome analysis with NGS.

Tools & Technology
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PCR
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Research & Discovery
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Gene Expression Research

Infrared detection decreases nitrocellulose autofluorescence and improves RPPA assays signal‐to‐noise ratio over visible wavelength detection

Protein array applications in disease biomarker discovery and validation reflect the enormous potential of protein arrays in the field of personalized medicine. Until now, the rise of protein array technology was limited by high fluorescence emitted by nitrocellulose. The InnoScan 710-IR infrared microarray scanner now allows an increased signal-to-noise ratio and thus sensitivity of RPPAs by decreasing background fluorescence. In addition, with a high resolution of up to 3 µm per pixel, it allows the acquisition of high quality images.

Tools & Technology
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Microarrays & Multiplexing
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Research & Discovery
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Proteomics & Protein Research
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Biomarker Discovery & Validation

Automated RT-qPCR Utilizing the Access Workstation, the Echo Liquid Handler, and RealTime Ready Reagents from Roche Applied Science

RT-qPCR has been increasingly utilized by researchers to quantify mRNA levels. Its widespread use has been limited by an often laborious multi-step process and high reagent cost. Recent advances in non-contact reagent dispensing and next generation one step lysis reagents are enabling scientists to generate high throughput data at a much faster rate. This technical note describes the automation of three complementary tools to generate high throughout RT-qPCR data; the Echo liquid handler, RealTime Ready cell lysis reagents, and the Access workstation.

Tools & Technology
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PCR
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Gene Expression Research

Precise Sizing and SMRT Sequencing Offer Unprecedented Read Length for Clinical Studies

Using BluePippin significantly extends average read length for PacBio. Read this case study to learn how Robert Sebra at the Icahn Institute for Genomics and Multiscale Biology uses automated DNA size selection to maximize read length with SMRT Sequencing.

Tools & Technology
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Sequencing Technology
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Sample Prep

Conducting Clinical Next-Generation Sequencing: How to Manage Change, CLIA, NGS and Informatics

The drive toward personalized medicine has led many labs to consider conducting clinical tests employing next-generation sequencing, but the decision to do so requires labs to consider how they will conduct this work under the auspices of CLIA or CAP requirements. This paper outlines the general principles of CLIA certification and its specific application to clinical NGS, from the perspective of both research and clinical labs.

Tools & Technology
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Informatics
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Sequencing Technology

Assessing Quality Using ACCURUN Controls for Quantitative Viral Load Assays

ACCURUN controls from SeraCare Life Sciences are developed and manufactured as third-party controls. These products are designed to support the quality control procedures within clinical labs. When used properly and as part of an overall QC program, ACCURUN controls will monitor assay accuracy and precision, help identify performance issues and improve the work efficiency of a clinical lab. The ultimate goal of the QC program is to provide added confidence in the reliability and validity of the reported results.

Tools & Technology
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Research & Discovery

Increase User Adoption Rates and Realize a Higher Rate of Return on your LIMS Investment

Usability is the key to ensuring that LIMS are adopted and used, but many LIMS developers forget about the end user. This paper describes the traditional barriers to LIMS adoption and explains how these hurdles can be overcome by a focus on usability.

Tools & Technology
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Sequencing Technology

Miniaturization of Multiple Displacement Amplification of Genomes from a Single Cell

Advances in whole-genome amplification have enabled sequencing of DNA and RNA from a single cell, or what is commonly called Single-cell Genomics (SGC). Despite the growing interest in SGC, a standardized method for sample preparation currently does not exist. However in a recent Nature Protocols article, "Obtaining genomes from uncultivated environmental microorganisms using FACS-based single cell genomics," researchers at the Department of Energy Joint Genome Institute describe an approach that can meet the throughput and sample quality required for robust whole-genome amplification from a single cell. This application highlight describes the role of the Echo liquid handler in this new approach. 

Tools & Technology
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Sample Prep

High Throughput RT-qPCR for Gene Expression Analysis

The current standard of accuracy for quantification of gene expression is reverse transcriptase quantitative PCR (RT-qPCR). A new, cost-effective sample preparation method for RT-PCR incorporates a “one-step” cell lysis buffer which eliminates the need for mRNA isolation and purification. This improved method, when combined with nanoscale non-contact liquid handling technology enables a high throughput automated workflow for gene expression.

Tools & Technology
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PCR
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Gene Expression Research

Miniaturization of the KASP Genotyping Assay for Maize with the Echo 525 Liquid Handler

SNP genotyping of maize samples is commonly performed in agricultural science to aide marker assisted selection, study heterosis and a variety of biological behaviors. Its widespread adoption in agricultural science has been challenged with increasing reagent costs and labor intensive multi-step processes. Acoustic non-contact liquid handling using the Echo 525 liquid handler offers unique advantages to traditional processes by incorporating a tip-less solution to deliver reagents precisely and accurately. Assay miniaturization is enabled with high accuracy and precision at volumes as low as 25nL. This study utilized the Echo 525 liquid handler to miniaturize a KASP genotyping assay for maize at a throughput meeting the demands of most high throughput production processes.

Tools & Technology

RNAi Screening in Primary Cells

Screening approaches involving either overexpression or RNAi-mediated down-regulation of genes have become a potent tool for identifying drug targets. Such screens require transfection of cells with e.g. cDNA or shRNA vectors or siRNA oligonucleotides. One important factor for screening success is the ability to efficiently transfect biologically relevant cells. Lonza’s Nucleofector Technology is a proven non-viral method for efficient transfection of primary cells, e.g. human T cells. The HT Nucleofector System, a 384-well platform, expands its application range to high-throughput transfections. With its fast plate processing time and easy integration into liquid handling systems it is a convenient tool for siRNA, shRNA or miRNA screens in biologically relevant cell types. 

miRNA/RNAi
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Tools & Technology

Reverse Phase Protein Arrays for Cell Signaling: Using the InnoScan 710-IR scanner improves sensitivity and dynamic range.

Reverse Phase Protein Arrays (RPPAs) are increasingly used to study cell signaling as they are highly multiplexed and allow precise quantification of protein of interests in biological samples. Such arrays promote automation, simplified work flow, and preserve sample.  One of the principal challenges faced by RPPAs is to find the best combination of an array surface that will support high binding levels of viable protein probes, and a detection method that will provide high sensitivity and dynamic range. With the new InnoScan 710-IR scanner it is now possible to combine infrared detection with high sensitivity and quality images.

Tools & Technology
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Microarrays & Multiplexing
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Research & Discovery
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Proteomics & Protein Research

Miniaturizing siRNA Transfection Using the Echo Liquid Handler

Large-scale, high-throughput siRNA experiments require a transfer system that can facilitate reliable and reproducible transfections in high-density well-plate formats, as well as effective delivery of the siRNA molecule. This study demonstrates superior performance of the Echo liquid handler compared to more traditional liquid handling methods for standard, reverse and lipid-free transfection of siRNA molecules into mammalian cells. Results of the study clearly demonstrate the ability of the Echo liquid handler to deliver comparable transfection efficiency, knock-down and cell morphology to reactions prepared using traditional pipeting methods. In fact, reactions prepared with the Echo liquid handler were miniaturized to use significantly less volume of siRNA and other reagents, and still yielded more representative inclusion intensities than traditional manual pipetting techniques. Such miniaturization can result in significant cost savings and greater confidence in the results from siRNA screening studies.

Tools & Technology
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miRNA/RNAi

High-throughput Miniaturized Quantitative PCR with the Echo 525 Liquid Handler

Quantitative PCR (qPCR) is a prevalent tool spanning many phases of drug discovery. Advances in qPCR detection to enable 384- and 1536-well microplate formats have incentivized researchers to miniaturize qPCR assays as a means to offset the costs of increasing throughput. To significantly reduce qPCR volumes and maintain data quality, the liquid handling methods employed for such low-volume transfers must be precise and accurate. Tipless, touchless acoustic droplet ejection with the Echo liquid handler eliminates the cost of disposable tips or tip-wash cycles and simplifies assay setup by eliminating dilution steps. This study utilized the Echo 525 liquid handler to assemble low-volume qPCR assays at speeds that keep pace with high-throughput demands. The results demonstrated the Echo 525 liquid handler effectively miniaturized reaction volumes for high-throughput qPCR in both 384- and 1536-well formats.

Tools & Technology
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PCR

Scientists Use Pippin to Optimize Nextera Libraries

Learn how Pippin Prep can optimize your Nextera libraries In this case study, Zach Herbert at the Dana-Farber Cancer Institute describes adding automated DNA sizing from Sage Science to his Nextera workflow for better sequence results.

Sequencing Technology
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Tools & Technology
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Sample Prep

Reading the Writing on the Wall: Four Telltale Signs That You Might Need a LIMS

Many labs shy away from the notion of upgrading to a laboratory information management system because they are happy with spreadsheets, but if your lab is expanding, processing new samples, or offering new services, you may need to upgrade to a more formal or structured solution. This paper poses four questions for labs to determine if it's time to make the leap to a LIMS.

Tools & Technology
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Informatics

Life Science Storage & Data Management Guide

This white paper will distill many of observed storage and NGS data management related issues as well as the current expert perspective on the life science storage, NGS and data management landscape.

Tools & Technology
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Informatics

Taking NAS to the Cloud

The flood of genomic (and other life sciences) data has just begun. A central challenge for large and small organizations generating the massive data treasure trove is how to store and manage the data. This article discusses leveraging cloud storage for data deluge in the sciences.

Tools & Technology
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Informatics

Reducing the variability of pre-analytical handling of biological samples

The increasing use of biomarkers as diagnostic indicators of pathological conditions, as monitors of disease progression or as surrogate markers of patient outcomes in clinical trials has led to a huge increase in the number of biological samples whose accurate analysis is of vital importance...

Tools & Technology
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Sample Prep
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Clinical & Translational
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Biomarker Discovery & Validation

Randomized Adapters for Reducing Bias in Small RNA-Seq Libraries

While next-generation sequencing is the most practical method for identifying small RNAs, bias can skew the resulting data. Bioo Scientific has developed its NEXTflex Small RNA Sequencing Kit v2 to reduce this bias by incorporating a randomized adapter strategy that involves incorporating pools of adapters with randomized bases at critical positions adjacent to the ligation junctions. This application note details a validation study that demonstrates the reduced bias when using a randomized adapter strategy.  

Tools & Technology
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Sequencing Technology
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Sample Prep

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