Automated RT-qPCR Utilizing the Access™ Workstation, the Echo® Liquid Handler, and RealTime Ready™ Reagents from Roche Applied Science BY Labcyte
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.
August 2, 2013
Conducting Clinical Next-Generation Sequencing: How to Manage Change, CLIA, NGS and Informatics BY GenoLogics
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.
January 23, 2014
Continuous Collection of Stem Cells from a Human Placenta Perfusion Co-Culture BY FiberCell
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.
May 22, 2014
Cookie Cutter Proteolysis: Achieving Reproducible, Efficient Digestions for Proteomic Workflows BY Shimadzu
Protein sample preparation workflows for mass spectrometric analysis that involve proteolysis are often labor-intensive, time consuming, and user dependent. The introduction of variability hinders discovery initiatives. Recently, an automated protein digestion platform was developed that accelerates the digestion process while providing exceptional reproducibility. As demonstrated in this poster, it offers complete, reproducible protein digestions in as little as 30 seconds, allowing hundreds of samples to be run per day, and can be adapted to many applications.
July 24, 2013
Detecting Latent and Active HIV Using the RainDrop® Digital PCR System BY RainDance
Human Immunodeficiency Virus (HIV) expression has been observed at very low levels while active, and is even more difficult to detect when latent. Previous methods have involved testing for p24 antigens or antibodies (1) or RNA expression in the range of 20 to 40 copies per milliliter (2). This application note highlights the capability of the RainDrop Digital PCR system to detect active virus (RNA), latent virus (DNA), and human and viral targets together in a single reaction. In this application note, Human Universal RNA (BioChain, #R4234565-1), Xeno RNA (Cells-to-Ct kit, Life Technologies, #4386995) and de-identified samples from some of our key customers were evaluated to demonstrate the RainDrop's utility for sensitive, precise multiplex detection of HIV DNA or RNA.
July 7, 2014
Generating Scientific Insights Through Deep Collaboration BY BioFortis
In order to make data smarter, data exploration tools need to be placed in the hands of not only the IT and informatics experts but also the scientists and domain experts that understand and can act on the data, independent of knowing how to write programming code, the structure of data or even where it is located.
The Qiagram deep collaborative environment provides just such tools, allowing researchers to explore their own data in a collaborative, transparent and effective manner.
March 1, 2013
High Throughput RT-qPCR for Gene Expression Analysis BY Labcyte
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.
August 2, 2013
High-throughput Miniaturized Quantitative PCR with the Echo® 525 Liquid Handler BY Labcyte
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.
August 2, 2013
In Vitro Toxicology and Hollow Fiber Bioreactors BY FiberCell
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.
May 22, 2014
Increase User Adoption Rates and Realize a Higher Rate of Return on your LIMS Investment BY GenoLogics
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.
January 23, 2014
Infrared detection decreases nitrocellulose autofluorescence and improves RPPA assays signal‐to‐noise ratio over visible wavelength detection BY Innopsys
Advances in RPPA and more generally protein array technology have resulted in a rapidly growing market. Besides RPPAs there are also analytical and functional protein microarrays. 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 fluorscence. In addition, with a high resolution of up to 3µm per pixel, it allows the acquisition of high quality images.
August 12, 2013
Is Your Biobank Ready for the Challenge of Biomarker-based Research? BY BioFortis
For researchers involved in biomarker-based clinical and translational research, who need to safely and effectively conduct externalized, science-driven collaborative studies, BioFortis’ Next Generation Biobanking software platform harmonizes biospecimen data with clinical and molecular data in a collaborative environment that emphasizes scientific insights, while ensuring security and compliance.
March 1, 2013
Making single cell CTC analysis possible BY DeNovo
DeNovo Sciences is introducing its new proprietary JETTA microfluidic system that captures and sorts CTCs into individual compartments while allowing on-chip single cell, multiplexed molecular assays. Together with DeNovo’s Vanguard imaging station, this innovative technology makes high throughput, automatic processing of CTCs possible.
May 13, 2014
Miniaturization of Multiple Displacement Amplification (MDA) of Genomes from a Single Cell BY Labcyte
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). SGC has become an invaluable
approach to understanding the magnitude of genetic and epigenetic variation that occurs
throughout the life of an organism. 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 singlecell
1 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.
May 22, 2014
Miniaturization of the KASP™ Genotyping Assay for Maize with the Echo 525 Liquid Handler BY Labcyte
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.
September 26, 2013
Miniaturizing siRNA Transfection Using the Echo® Liquid Handler BY Labcyte
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.
August 2, 2013
Oracle Health Sciences Translational Research Center: A Translational Medicine Platform to Address the Big Data Challenge BY Oracle
Oracle Health Sciences Translational Research Center is a scalable informatics solution for translational research. Its back-end data components seamlessly integrate clinical and omics data from diverse clinical data sources as well as from vendor-specific and modality-specific omics data silos, providing standardized data readily available for the front-end application.
February 4, 2013
Precise Sizing and SMRT Sequencing Offer Unprecedented Read Length for Clinical Studies BY Sage Science
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.
March 7, 2014
Production of Large Quantities of Mouse and Rabbit Monoclonal Antibodies using the FiberCell Systems® Inc. Bioreactor BY FiberCell
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.
May 22, 2014
Production of Recombinant Proteins and Monoclonal Antibodies in Hollow Fiber Bioreactors BY FiberCell
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.
May 22, 2014
RainDance ThunderBolts™ Cancer Panel BY RainDance
The ThunderBolts Cancer Panel enables researchers to rapidly detect and cost-effectively analyze mutations on precious FFPE (Formalin-Fixed Paraffin-Embedded), and Fluid Biopsy™ samples (circulating tumor DNA or ctDNA). The ThunderBolts Cancer Panel uses single molecule PCR to target 50 known cancer genes including tumor suppressors, mutation hotspots and drug resistance markers. The panel also features industry breakthroughs in sequence coverage and uniformity, allelic sensitivity, sample flexibility, workflow, and cost.
July 7, 2014
RainDrop® Digital PCR BY RainDance
Capable of generating more than a billion reactions in a single day, the RainDrop Digital PCR System surpasses all existing technologies and establishes a new performance standard in sensitivity, quantification, and multiplexing. Based on RainDance's proven digital droplet platform, the RainDrop System delivers absolute quantification of target molecules. The RainDrop Digital PCR System fundamentally changes the performance of molecular assays by enabling digital answers across a number of important research applications including low-frequency tumor allele detection, absolute quantification of expression profiles or DNA copy numbers, SNP measurement, and viral quantification.
July 9, 2014
Reading the Writing on the Wall: Four Telltale Signs That You Might Need a LIMS BY GenoLogics
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.
February 19, 2014
Reducing the variability of pre-analytical handling of biological samples BY BioCision
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...
April 26, 2012
Reverse Phase Protein Arrays for Cell Signaling: Using the InnoScan 710-IR scanner improves sensitivity and dynamic range. BY Innopsys
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.
May 22, 2013
RNAi Screening in Primary Cells BY Lonza
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.
July 29, 2013
Scientists Use Pippin to Optimize Nextera Libraries BY Sage Science
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.
March 7, 2014
Technical Note: A New Method of Snap Freezing Bacteria Using BioCision’s CoolRack System BY BioCision
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...
April 26, 2012
ThunderStorm® System BY RainDance
The RainDance ThunderStorm® System enables researchers to apply gold-standard PCR more cost-effectively and at higher throughput using any next-generation sequencing platform. The system leverages RainDance's proven single molecule PCR technology that generates millions of unique picodroplet PCR reactions and enables scientists to target up to 20,000 PCR amplicons in a single sample. The system features true walkaway capabilities that will automatically process up to 96 samples in a single run and access up to eight different primer panels. When combined with RainDance's sophisticated primer design pipeline and high-value consumables and reagents, the ThunderStorm System ensures high daily sample throughput, best-in-class target coverage and uniformity, with attractive running economics and minimal hands-on time.
July 9, 2014