The document introduces the OpenArray platform developed by BioTrove for parallel, low-volume nucleic acid reactions. Key features of the OpenArray include its microarray-like format of 3072 through-holes that can perform individual 33nL reactions, enabling high-throughput genotyping and gene expression analysis. The platform offers flexibility to customize assays and samples, low reagent usage, and ease of use. Potential applications discussed include life sciences research, pathogen surveillance and detection, and future directions in molecular diagnostics.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.3- Introduction to NGS Variant Calling Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Updated: New High Throughput Sequencing technologies at the Norwegian Sequenc...Lex Nederbragt
Un update of the previous talk with the same title. A talk I gave at the Computational Life Science initiative (University of Oslo) about new High Throughput Sequencing instruments at the Norwegian Sequencing Centre. I also mentioned future upgrades, and the upcoming nanopore sequencing platform of Oxford nanopore.
1. Next-generation sequencing methods such as Roche 454, Illumina GAII, and ABI SOLiD allow for high throughput DNA sequencing through massive parallel sequencing.
2. These methods involve clonal amplification of DNA fragments on solid surfaces or in emulsion PCR followed by sequencing using pyrosequencing, sequencing by synthesis with reversible terminators, or sequencing by ligation approaches.
3. The resulting sequencing data requires high throughput management and analysis pipelines to process the large volumes of sequence data produced.
xGen® target capture products from IDT enable greater sensitivity and higher sample throughput for targeted next generation sequencing (NGS). NGS researchers can now benefit from the IDT high throughput, quality controlled manufacturing process to order gene panels that have the greatest level of uniformity. These panels can be easily optimized with the addition of more probes.
Learn more at http://www.idtdna.com/xgen
Improved Reagents & Methods for Target Enrichment in Next Generation Sequencing, presented by Dr Mark Behlke, Chief Scientific Officer at Integrated DNA Technologies
The document summarizes a study that used Illumina Hi-seq sequencing to analyze taxon diversity in bulk insect samples. The researchers tested two approaches: 1) PCR-based amplification of the COI barcode region followed by Illumina sequencing, and 2) direct shotgun sequencing of total mitochondrial DNA without PCR. Both approaches showed potential for high-throughput environmental barcoding, though methodological improvements are still needed to address issues like taxonomic and biomass biases. The study demonstrates that Illumina sequencing can perform comparably to other platforms for analyzing mixed insect samples and may help solve amplification biases through a PCR-free method.
The increasing throughput of NGS platforms has fueled the demand to sequence many samples in parallel, also referred to as multiplex sequencing. During multiplex sequencing, the identity of each sample library within a pool is maintained using index sequences that are subsequently separated in a process called demultiplexing during data analysis. Historically, a relatively small number of unique sequences (8 x i5 and 12 x i7) were used to create index combinations to multiplex samples. Unfortunately, with this combinatorial approach, a single index swap may cause a read to be mis-assigned to a different sample causing cross-talk. In this presentation, we discuss some sources of sample cross-talk, including index hopping during cluster amplification or multiplexed capture, and how index sequencing errors may lead to demultiplexing mistakes. We discuss how sample cross-talk causes demultiplexing errors and present a method for increasing the accuracy of sample identification using unique, dual-matched index adapters.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.3- Introduction to NGS Variant Calling Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Updated: New High Throughput Sequencing technologies at the Norwegian Sequenc...Lex Nederbragt
Un update of the previous talk with the same title. A talk I gave at the Computational Life Science initiative (University of Oslo) about new High Throughput Sequencing instruments at the Norwegian Sequencing Centre. I also mentioned future upgrades, and the upcoming nanopore sequencing platform of Oxford nanopore.
1. Next-generation sequencing methods such as Roche 454, Illumina GAII, and ABI SOLiD allow for high throughput DNA sequencing through massive parallel sequencing.
2. These methods involve clonal amplification of DNA fragments on solid surfaces or in emulsion PCR followed by sequencing using pyrosequencing, sequencing by synthesis with reversible terminators, or sequencing by ligation approaches.
3. The resulting sequencing data requires high throughput management and analysis pipelines to process the large volumes of sequence data produced.
xGen® target capture products from IDT enable greater sensitivity and higher sample throughput for targeted next generation sequencing (NGS). NGS researchers can now benefit from the IDT high throughput, quality controlled manufacturing process to order gene panels that have the greatest level of uniformity. These panels can be easily optimized with the addition of more probes.
Learn more at http://www.idtdna.com/xgen
Improved Reagents & Methods for Target Enrichment in Next Generation Sequencing, presented by Dr Mark Behlke, Chief Scientific Officer at Integrated DNA Technologies
The document summarizes a study that used Illumina Hi-seq sequencing to analyze taxon diversity in bulk insect samples. The researchers tested two approaches: 1) PCR-based amplification of the COI barcode region followed by Illumina sequencing, and 2) direct shotgun sequencing of total mitochondrial DNA without PCR. Both approaches showed potential for high-throughput environmental barcoding, though methodological improvements are still needed to address issues like taxonomic and biomass biases. The study demonstrates that Illumina sequencing can perform comparably to other platforms for analyzing mixed insect samples and may help solve amplification biases through a PCR-free method.
The increasing throughput of NGS platforms has fueled the demand to sequence many samples in parallel, also referred to as multiplex sequencing. During multiplex sequencing, the identity of each sample library within a pool is maintained using index sequences that are subsequently separated in a process called demultiplexing during data analysis. Historically, a relatively small number of unique sequences (8 x i5 and 12 x i7) were used to create index combinations to multiplex samples. Unfortunately, with this combinatorial approach, a single index swap may cause a read to be mis-assigned to a different sample causing cross-talk. In this presentation, we discuss some sources of sample cross-talk, including index hopping during cluster amplification or multiplexed capture, and how index sequencing errors may lead to demultiplexing mistakes. We discuss how sample cross-talk causes demultiplexing errors and present a method for increasing the accuracy of sample identification using unique, dual-matched index adapters.
my students use ideas from my class on business models to develop a business model for ion proton's DNA sequencer. This sequencer uses semiconductor technology to read an organism's DNA sequence and is faster and cheaper than existing sequencers. This presentation describes the value proposition, customer selection, method of value capture and other aspects of a business model for Ion Proton's DNA sequencer
Visit Life Technologies -> http://owl.li/ggoaG to learn more about how we provide a complete range of solutions for addressing 21st century agricultural biotechnology challenges. From de novo and transcriptome sequencing, to molecular breeding and genotyping, to precise genome engineering, see how our products are rapidly accelerating the field of plant and animal genetics in this resource guide that provides an overview of the applications that Life Technologies plant sciences products support. Look for Life Technologies at the Plant and Animal Genome Conference each year to see the latest agricultural technologies up close in our booth.
The document describes a collection of lentiviral ORF clones called Precision LentiORFs contained in the pLOC lentiviral vector. Key features include:
- The ORF, fluorescent marker, and selection marker are expressed from one promoter for tracking ORF expression.
- It provides two methods (fluorescent marker and antibiotic resistance) to optimize transduction.
- The vector allows addition of fusion tags and works with both transfection and transduction for ORF expression in a variety of cell types.
- Protocols are provided for replicating plates of clones stored in glycerol stock and preparing plasmid DNA from individual clones.
IDT provides a range of solutions for targeted next generation sequencing. Labs processing hundreds to thousands of samples can create highly uniform, custom panels using xGen® Lockdown Probes. The new xGen Acute Myeloid Leukemia (AML) panel is a predesigned set of Lockdown Probes that captures 260 genes identified by whole genome and exome sequencing of 200 patient samples. The AML panel can be used as stand-alone or customized with additional probes to detect other targets of interest.
The document describes xGen Predesigned Gene Capture Pools, which are pools of xGen Lockdown Probes designed to target specific genes. The pools offer advantages over custom panels such as better customization ability, decreased optimization time, and lower cost. They can be used to build custom gene panels, supplement existing panels, and share targets between researchers studying different diseases. Data shows the pools provide high on-target performance, consistent deep coverage, and can supplement existing panels without affecting coverage.
Next generation sequencing: research opportunities and bioinformatic challenges. A seminar I gave for the Computational Life Science (Univ. of Oslo) seminar series, March 2, 2011
Presentation used for my oral Master's Thesis defense for the Universtat Autònoma de Barcelona. It shows the development of a Perl script for the automated generation of a report of the somatic mutations found in a Normal/Tumor cancer experiment.
Advances and Applications Enabled by Single Cell TechnologyQIAGEN
Over the past 5 years, single-cell genomics have become a powerful technology for studying small samples and rare cells, and for dissecting complex populations such as heterogeneous tumors. Single-cell technology is enabling many new insights into diverse research areas from oncology, immunology and microbiology to neuroscience, stem cell and developmental biology. This webinar introduces single-cell technology and summarizes the newest scientific applications in various research areas, all in the context of current literature.
1) The document discusses different whole genome amplification techniques for obtaining DNA from single cells, including PCR-based and PCR-free methods.
2) It provides comparisons of different whole genome amplification kits, finding that QIAGEN's REPLI-g Single Cell Kit has the highest genome coverage, lowest duplication rates, and best performance for detecting copy number variations and single nucleotide variations, making it optimal for single cell sequencing applications.
3) Case studies demonstrate that the REPLI-g Single Cell Kit provides more uniform coverage and significantly fewer sequencing errors compared to the MALBAC method.
Reproducible bioinformatics pipelines with Docker and AndurilChristian Frech
Christian Frech presented on using Docker and Anduril to create reproducible bioinformatics pipelines. Anduril is a pipeline framework that aims to make pipelines modular, bundled with their execution environment, and able to be run on clusters. It uses a proprietary scripting language but can embed other languages. Frech demonstrated an RNA-seq analysis pipeline built in Anduril, which generated QC plots, differential expression results, network and enrichment analyses. While adoption of Anduril has been limited by its scripting language, Docker can be used to containerize components and make pipelines fully reproducible and portable.
Performance of a Prototype Rapid, Point-of-Care Test* for Identifying HIV Inf...CDC NPIN
The document describes a prototype for a next generation rapid HIV test developed by OraSure Technologies. The prototype aims to detect HIV antibodies earlier than current rapid tests by achieving sensitivity similar to 3rd generation ELISA tests while maintaining a 10-minute test time. Performance studies showed the prototype detected HIV antibodies earlier than a FDA-approved rapid test in 50% of seroconversion panels tested, with an average of 5 days earlier detection. Specificity of the prototype was 99.87% in plasma samples. The prototype achieved all design goals of earlier detection of HIV antibodies during acute infection and a reduced test time.
The rapid increase in throughput of next generation sequencing (NGS) platforms is changing the genomics landscape. Typically, adapters containing sample indexes are added during library construction to allow multiple samples to be sequenced in parallel. Some strategies also introduce a unique molecular identifier (UMI) within the adapter to correct for PCR and sequencing errors. When a UMI is added, reads are assigned to each sample based on their associated sample index, and the UMI is used for error correction during data analysis. For simplicity, a single adapter that is suitable for a variety of applications would be ideal.
xGen® Dual Index UMI Adapters take the guesswork out of adapter design and ordering. These adapters, created for Illumina sequencers, are compatible with standard library preparation methods and may be sequenced in different modes depending on your application. In addition to unique, dual indexes, the adapters contain a molecular barcode in an optional read position. We will discuss how unique, dual indexes mitigate sample index hopping for multiplexed sequencing and demonstrate how UMIs reduce false positives to improve detection of low-frequency variants.
20 Ideas for your Website Homepage ContentBarry Feldman
Perplexed about what to put on your website home? Every company deals with this tough challenge. The 20 ideas in this presentation should give you a strong starting point.
This document outlines 50 essential content marketing hacks presented by Matt Heinz, President of Heinz Marketing Inc. at CMWorld. It provides an agenda for the presentation and covers topics such as content planning, measurement, formats, distribution, influencer engagement, repurposing content, and getting sales teams to leverage content. The goal is to provide new tools, tricks and best practices to help convert readers into customers through effective content marketing.
The document discusses prototyping and provides examples of different types of prototypes including paper prototypes, digital prototypes, storyboards, role plays, and space prototypes. It explains that prototyping is used to make ideas tangible and test reactions from users in order to gain insights. Prototypes should be iterated on and fail early to push ideas further and save time and money. Both low and high fidelity prototypes are mentioned as ways to test ideas at different stages of the design process.
10 Insightful Quotes On Designing A Better Customer ExperienceYuan Wang
In an ever-changing landscape of one digital disruption after another, companies and organisations are looking for new ways to understand their target markets and engage them better. Increasingly they invest in user experience (UX) and customer experience design (CX) capabilities by working with a specialist UX agency or developing their own UX lab. Some UX practitioners are touting leaner and faster ways of developing customer-centric products and services, via methodologies such as guerilla research, rapid prototyping and Agile UX. Others seek innovation and fulfilment by spending more time in research, being more inclusive, and designing for social goods.
Experience is more than just an interface. It is a relationship, as well as a series of touch points between your brand and your customer. Here are our top 10 highlights and takeaways from the recent UX Australia conference to help you transform your customer experience design.
For full article, continue reading at https://yump.com.au/10-ways-supercharge-customer-experience-design/
How to Build a Dynamic Social Media PlanPost Planner
Stop guessing and wasting your time on networks and strategies that don’t work!
Join Rebekah Radice and Katie Lance to learn how to optimize your social networks, the best kept secrets for hot content, top time management tools, and much more!
Watch the replay here: bit.ly/socialmedia-plan
http://inarocket.com
Learn BEM fundamentals as fast as possible. What is BEM (Block, element, modifier), BEM syntax, how it works with a real example, etc.
The document discusses how personalization and dynamic content are becoming increasingly important on websites. It notes that 52% of marketers see content personalization as critical and 75% of consumers like it when brands personalize their content. However, personalization can create issues for search engine optimization as dynamic URLs and content are more difficult for search engines to index than static pages. The document provides tips for SEOs to help address these personalization and SEO challenges, such as using static URLs when possible and submitting accurate sitemaps.
The document describes the OpenArray technology on the QuantStudio 12K Flex Real-Time PCR System. It allows for high-throughput gene expression profiling, screening, and confirmation through mid-density PCR plates. A single user can now complete most projects in days instead of weeks, generating over 12,000 data points in a single run. It provides fast, high-throughput, and cost-effective analysis for applications like genotyping, gene expression, miRNA profiling, and digital PCR.
Protein microarrays allow the immobilization and detection of large numbers of proteins on small surfaces. Three key steps in the protein microarray workflow are printing, surface selection, and imaging. Optimizing the printing process is important to minimize contamination between samples. The Omnigrid and Microgrid systems can print contact-style onto 3D substrates with controls to reduce surface damage. Multiplexed protein microarrays on plates allow high-throughput screening by testing many samples in parallel. NovaRay imaging supports multiple array formats and wavelengths for detection. An example experiment showed specific and reproducible detection of target proteins in individual wells of a multiplexed plate with no carryover between wells.
This white paper describes SABiosciences' Oligo GEArray DNA microarray system. Key points:
1) Oligo GEArrays profile gene expression of focused gene panels (113-440 genes) related to biological pathways or disease states, providing a more economical alternative to genome-wide microarrays.
2) The system uses flexible target labeling kits, membrane arrays, and a simple chemiluminescent detection method, allowing it to be easily adopted in any laboratory.
3) Data shows the Oligo GEArray has high sensitivity (can detect 10 fM targets), a wide dynamic range, and is highly reproducible, with technical replicates yielding CVs less than 10%.
my students use ideas from my class on business models to develop a business model for ion proton's DNA sequencer. This sequencer uses semiconductor technology to read an organism's DNA sequence and is faster and cheaper than existing sequencers. This presentation describes the value proposition, customer selection, method of value capture and other aspects of a business model for Ion Proton's DNA sequencer
Visit Life Technologies -> http://owl.li/ggoaG to learn more about how we provide a complete range of solutions for addressing 21st century agricultural biotechnology challenges. From de novo and transcriptome sequencing, to molecular breeding and genotyping, to precise genome engineering, see how our products are rapidly accelerating the field of plant and animal genetics in this resource guide that provides an overview of the applications that Life Technologies plant sciences products support. Look for Life Technologies at the Plant and Animal Genome Conference each year to see the latest agricultural technologies up close in our booth.
The document describes a collection of lentiviral ORF clones called Precision LentiORFs contained in the pLOC lentiviral vector. Key features include:
- The ORF, fluorescent marker, and selection marker are expressed from one promoter for tracking ORF expression.
- It provides two methods (fluorescent marker and antibiotic resistance) to optimize transduction.
- The vector allows addition of fusion tags and works with both transfection and transduction for ORF expression in a variety of cell types.
- Protocols are provided for replicating plates of clones stored in glycerol stock and preparing plasmid DNA from individual clones.
IDT provides a range of solutions for targeted next generation sequencing. Labs processing hundreds to thousands of samples can create highly uniform, custom panels using xGen® Lockdown Probes. The new xGen Acute Myeloid Leukemia (AML) panel is a predesigned set of Lockdown Probes that captures 260 genes identified by whole genome and exome sequencing of 200 patient samples. The AML panel can be used as stand-alone or customized with additional probes to detect other targets of interest.
The document describes xGen Predesigned Gene Capture Pools, which are pools of xGen Lockdown Probes designed to target specific genes. The pools offer advantages over custom panels such as better customization ability, decreased optimization time, and lower cost. They can be used to build custom gene panels, supplement existing panels, and share targets between researchers studying different diseases. Data shows the pools provide high on-target performance, consistent deep coverage, and can supplement existing panels without affecting coverage.
Next generation sequencing: research opportunities and bioinformatic challenges. A seminar I gave for the Computational Life Science (Univ. of Oslo) seminar series, March 2, 2011
Presentation used for my oral Master's Thesis defense for the Universtat Autònoma de Barcelona. It shows the development of a Perl script for the automated generation of a report of the somatic mutations found in a Normal/Tumor cancer experiment.
Advances and Applications Enabled by Single Cell TechnologyQIAGEN
Over the past 5 years, single-cell genomics have become a powerful technology for studying small samples and rare cells, and for dissecting complex populations such as heterogeneous tumors. Single-cell technology is enabling many new insights into diverse research areas from oncology, immunology and microbiology to neuroscience, stem cell and developmental biology. This webinar introduces single-cell technology and summarizes the newest scientific applications in various research areas, all in the context of current literature.
1) The document discusses different whole genome amplification techniques for obtaining DNA from single cells, including PCR-based and PCR-free methods.
2) It provides comparisons of different whole genome amplification kits, finding that QIAGEN's REPLI-g Single Cell Kit has the highest genome coverage, lowest duplication rates, and best performance for detecting copy number variations and single nucleotide variations, making it optimal for single cell sequencing applications.
3) Case studies demonstrate that the REPLI-g Single Cell Kit provides more uniform coverage and significantly fewer sequencing errors compared to the MALBAC method.
Reproducible bioinformatics pipelines with Docker and AndurilChristian Frech
Christian Frech presented on using Docker and Anduril to create reproducible bioinformatics pipelines. Anduril is a pipeline framework that aims to make pipelines modular, bundled with their execution environment, and able to be run on clusters. It uses a proprietary scripting language but can embed other languages. Frech demonstrated an RNA-seq analysis pipeline built in Anduril, which generated QC plots, differential expression results, network and enrichment analyses. While adoption of Anduril has been limited by its scripting language, Docker can be used to containerize components and make pipelines fully reproducible and portable.
Performance of a Prototype Rapid, Point-of-Care Test* for Identifying HIV Inf...CDC NPIN
The document describes a prototype for a next generation rapid HIV test developed by OraSure Technologies. The prototype aims to detect HIV antibodies earlier than current rapid tests by achieving sensitivity similar to 3rd generation ELISA tests while maintaining a 10-minute test time. Performance studies showed the prototype detected HIV antibodies earlier than a FDA-approved rapid test in 50% of seroconversion panels tested, with an average of 5 days earlier detection. Specificity of the prototype was 99.87% in plasma samples. The prototype achieved all design goals of earlier detection of HIV antibodies during acute infection and a reduced test time.
The rapid increase in throughput of next generation sequencing (NGS) platforms is changing the genomics landscape. Typically, adapters containing sample indexes are added during library construction to allow multiple samples to be sequenced in parallel. Some strategies also introduce a unique molecular identifier (UMI) within the adapter to correct for PCR and sequencing errors. When a UMI is added, reads are assigned to each sample based on their associated sample index, and the UMI is used for error correction during data analysis. For simplicity, a single adapter that is suitable for a variety of applications would be ideal.
xGen® Dual Index UMI Adapters take the guesswork out of adapter design and ordering. These adapters, created for Illumina sequencers, are compatible with standard library preparation methods and may be sequenced in different modes depending on your application. In addition to unique, dual indexes, the adapters contain a molecular barcode in an optional read position. We will discuss how unique, dual indexes mitigate sample index hopping for multiplexed sequencing and demonstrate how UMIs reduce false positives to improve detection of low-frequency variants.
20 Ideas for your Website Homepage ContentBarry Feldman
Perplexed about what to put on your website home? Every company deals with this tough challenge. The 20 ideas in this presentation should give you a strong starting point.
This document outlines 50 essential content marketing hacks presented by Matt Heinz, President of Heinz Marketing Inc. at CMWorld. It provides an agenda for the presentation and covers topics such as content planning, measurement, formats, distribution, influencer engagement, repurposing content, and getting sales teams to leverage content. The goal is to provide new tools, tricks and best practices to help convert readers into customers through effective content marketing.
The document discusses prototyping and provides examples of different types of prototypes including paper prototypes, digital prototypes, storyboards, role plays, and space prototypes. It explains that prototyping is used to make ideas tangible and test reactions from users in order to gain insights. Prototypes should be iterated on and fail early to push ideas further and save time and money. Both low and high fidelity prototypes are mentioned as ways to test ideas at different stages of the design process.
10 Insightful Quotes On Designing A Better Customer ExperienceYuan Wang
In an ever-changing landscape of one digital disruption after another, companies and organisations are looking for new ways to understand their target markets and engage them better. Increasingly they invest in user experience (UX) and customer experience design (CX) capabilities by working with a specialist UX agency or developing their own UX lab. Some UX practitioners are touting leaner and faster ways of developing customer-centric products and services, via methodologies such as guerilla research, rapid prototyping and Agile UX. Others seek innovation and fulfilment by spending more time in research, being more inclusive, and designing for social goods.
Experience is more than just an interface. It is a relationship, as well as a series of touch points between your brand and your customer. Here are our top 10 highlights and takeaways from the recent UX Australia conference to help you transform your customer experience design.
For full article, continue reading at https://yump.com.au/10-ways-supercharge-customer-experience-design/
How to Build a Dynamic Social Media PlanPost Planner
Stop guessing and wasting your time on networks and strategies that don’t work!
Join Rebekah Radice and Katie Lance to learn how to optimize your social networks, the best kept secrets for hot content, top time management tools, and much more!
Watch the replay here: bit.ly/socialmedia-plan
http://inarocket.com
Learn BEM fundamentals as fast as possible. What is BEM (Block, element, modifier), BEM syntax, how it works with a real example, etc.
The document discusses how personalization and dynamic content are becoming increasingly important on websites. It notes that 52% of marketers see content personalization as critical and 75% of consumers like it when brands personalize their content. However, personalization can create issues for search engine optimization as dynamic URLs and content are more difficult for search engines to index than static pages. The document provides tips for SEOs to help address these personalization and SEO challenges, such as using static URLs when possible and submitting accurate sitemaps.
The document describes the OpenArray technology on the QuantStudio 12K Flex Real-Time PCR System. It allows for high-throughput gene expression profiling, screening, and confirmation through mid-density PCR plates. A single user can now complete most projects in days instead of weeks, generating over 12,000 data points in a single run. It provides fast, high-throughput, and cost-effective analysis for applications like genotyping, gene expression, miRNA profiling, and digital PCR.
Protein microarrays allow the immobilization and detection of large numbers of proteins on small surfaces. Three key steps in the protein microarray workflow are printing, surface selection, and imaging. Optimizing the printing process is important to minimize contamination between samples. The Omnigrid and Microgrid systems can print contact-style onto 3D substrates with controls to reduce surface damage. Multiplexed protein microarrays on plates allow high-throughput screening by testing many samples in parallel. NovaRay imaging supports multiple array formats and wavelengths for detection. An example experiment showed specific and reproducible detection of target proteins in individual wells of a multiplexed plate with no carryover between wells.
This white paper describes SABiosciences' Oligo GEArray DNA microarray system. Key points:
1) Oligo GEArrays profile gene expression of focused gene panels (113-440 genes) related to biological pathways or disease states, providing a more economical alternative to genome-wide microarrays.
2) The system uses flexible target labeling kits, membrane arrays, and a simple chemiluminescent detection method, allowing it to be easily adopted in any laboratory.
3) Data shows the Oligo GEArray has high sensitivity (can detect 10 fM targets), a wide dynamic range, and is highly reproducible, with technical replicates yielding CVs less than 10%.
This document provides an overview of immuno-PCR (I-PCR), which combines the antibody-based specificity of ELISA with the amplification power of PCR for highly sensitive antigen detection. Key points covered include: advantages and limitations of ELISA and real-time PCR; the main steps of I-PCR including antibody-oligonucleotide conjugation; and Innova Biosciences' ThunderLink PLUS technology for easy conjugation without specialist knowledge in 30 minutes. The presentation aims to introduce audiences to I-PCR and its applications in sensitive protein detection.
The BioTek Epoch Multi-Volume Spectrophotometer System allows for quantification of nucleic acids, proteins, and cell-based assays across a range of sample volumes from 2 μL to standard cuvettes. It bridges high performance monochromator readers and lower cost filter readers with excellent UV/Vis measurements in a compact design. The included Take3 Multi-Volume Plate enables measurements of up to 16 small-volume samples as well as BioCells and cuvettes.
protein microarray-types and approaches.pptxSachin Teotia
Protein microarrays are a high-throughput technology that allows thousands of proteins to be analyzed simultaneously. They consist of a solid support coated with thousands of different proteins in a defined array. Each protein spot represents a different protein. Protein microarrays can be used to study protein expression levels, interactions, activities, and functions on a large scale. There are different types including analytical, functional, and reverse-phase microarrays that each have their own strengths and applications.
BioOutsource is a company that provides testing services for biologics and vaccines to ensure quality and safety. They offer a unique combination of scientific expertise and innovative IT solutions embedded in a GMP-compliant environment. Services include cell-based assays for safety and potency testing of vaccines and biologics, molecular biology techniques like PCR for virus detection and residual DNA testing, and analytical protein tests. All services are performed according to GMP standards using validated methods. Client documentation and test results are securely stored and accessible through their web-based system.
The RA802 Pharmaceutical Analyser combines Renishaw's proprietary LiveTrackTM and StreamLineTM technologies to generate chemical images up to 150 times faster than conventional methods, whilst maintaining focus ? ensuring high quality pharmaceutical tablet imaging.
Functional genomics uses genome-wide experimental approaches to assess gene function on a large scale. It analyzes gene expression through techniques like transcriptomics and proteomics. Transcriptomics analyzes gene expression profiles through RNA sequencing or microarray analysis. Microarray analysis involves hybridizing fluorescently-labeled cDNA or cRNA to microarrays containing DNA probes to measure gene expression levels across thousands of genes simultaneously. Functional genomics provides a global understanding of gene function and molecular interactions through integrated omics approaches.
The document discusses marker-assisted breeding and the services provided by the Sequencing and Genotyping Platform. It outlines the steps in marker-assisted selection, from laying out seedlings and collecting samples to running analyses. It also lists the facilities and equipment available, including robotic platforms for liquid handling and DNA/RNA extraction, real-time PCR systems, capillary sequencers, and Illumina platforms for high-throughput genotyping. The platform provides support for marker-assisted breeding programs through services like whole genome sequencing, targeted resequencing, and protocol development for next-generation sequencing applications.
This document discusses various laboratory techniques for rapidly diagnosing and identifying microbes. It begins by explaining the need for rapid diagnosis and then describes several identification methods including biochemical profiling, API strips, BD BBL crystals, Vitek systems, Biolog, and MIDI Sherlock. These methods vary in their automation, databases, turnaround times, and whether they require gram stains but all aim to more quickly and accurately identify unknown microbes. The document concludes that automated systems have made analysis more reliable and reduced time and labor compared to older techniques.
BioOutsource provides in vitro virus safety testing services to test for potential virus contamination in biologic products and vaccines produced using mammalian cell culture systems. Their assays can test a variety of product types for viruses. Their GMP compliant facilities and services in the UK have been inspected by the MHRA. They offer validated assays to detect a broad spectrum of potential contaminants in compliance with various regulatory guidance. Their services provide fully GMP compliant testing with validated cell lines and virus banks, experienced personnel, and online reporting of results.
RT2 Profiler PCR Arrays are a real-time PCR technology that allows researchers to study gene expression patterns across biological pathways and processes. The arrays contain pre-designed primer assays for 84 relevant genes as well as controls on a single plate in a 96-well format. The gene content of the arrays is selected based on biological relevance and published associations with relevant pathways. The primer assays on the arrays undergo extensive validation for sensitivity, specificity, reproducibility, and amplification efficiency. The PCR Array system also includes optimized components for RNA isolation, cDNA synthesis, and real-time PCR to provide a complete validated workflow for gene expression analysis from sample to results.
Next Generation Diagnostics: Potential Clinical Applications of Illumina’sTec...Ilya Klabukov
Illumina's technology has potential clinical applications in molecular diagnostics. Their sequencing platforms like MiSeq and analysis software like KaryoStudioDx can enable molecular cytogenetic testing and targeted gene panels. MiSeq allows scalable amplicon sequencing from hundreds to thousands of targets in 1-2 days at lower costs than Sanger sequencing. Illumina aims to submit their iScan platform and arrays for FDA approval for post-natal cytogenetic testing. Their SNP microarrays can detect more types of chromosomal abnormalities than microarrays and help characterize regions associated with disease.
The GeneDisc Rapid Microbiology System provides microbial test results in as little as two hours using quantitative PCR technology. The system consists of a DNA Extractor that prepares samples, GeneDisc plates that are loaded into a GeneDisc Cycler for analysis. It tests for key pathogens in biopharmaceuticals, foods, and water. The system offers simplicity, speed, security of results, and cost savings compared to traditional methods.
This document discusses testing cell culture products for mycoplasma using polymerase chain reaction (PCR) techniques, which provide an alternative to traditional cell culture or growth media testing methods. PCR allows for rapid, sensitive and specific detection of mycoplasma nucleic acid sequences. Validation is required to replace the traditional methods with PCR to ensure it meets regulatory guidelines in terms of detecting a range of mycoplasma species and limiting false positives from contaminating DNA. The document also describes a validated commercial PCR kit that can be used along with controls and extraction validation to test for mycoplasma according to European Pharmacopoeia standards.
BioOutsource offers extensive cell bank characterization and safety testing services according to GMP standards. Their team has significant scientific expertise in evaluating master, working, and end-of-production cell banks used to manufacture biologics and vaccines. BioOutsource utilizes a variety of assays to test for identity, sterility, mycoplasma, adventitious agents, retroviruses, and species-specific pathogens. They provide customized testing plans and detailed reports to ensure cell banks are safe for use in human clinical trials. In addition, BioOutsource maintains a secure online portal where clients can access study documents, reports, and testing data.
Next-generation sequencing course, part 1: technologiesJan Aerts
This document provides an overview of next-generation sequencing technologies and their applications. It discusses genome enrichment techniques to isolate targeted regions for sequencing. It also describes template preparation methods like emulsion PCR and solid-phase amplification. Finally, it reviews various sequencing platforms like Illumina, SOLiD, 454 and details the sequencing and imaging processes. There are exercises proposed to work with sequencing data files in Galaxy.
Trusted Execution Environment for Decentralized Process MiningLucaBarbaro3
Presentation of the paper "Trusted Execution Environment for Decentralized Process Mining" given during the CAiSE 2024 Conference in Cyprus on June 7, 2024.
A Comprehensive Guide to DeFi Development Services in 2024Intelisync
DeFi represents a paradigm shift in the financial industry. Instead of relying on traditional, centralized institutions like banks, DeFi leverages blockchain technology to create a decentralized network of financial services. This means that financial transactions can occur directly between parties, without intermediaries, using smart contracts on platforms like Ethereum.
In 2024, we are witnessing an explosion of new DeFi projects and protocols, each pushing the boundaries of what’s possible in finance.
In summary, DeFi in 2024 is not just a trend; it’s a revolution that democratizes finance, enhances security and transparency, and fosters continuous innovation. As we proceed through this presentation, we'll explore the various components and services of DeFi in detail, shedding light on how they are transforming the financial landscape.
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1. :
Introduction to the OpenArray™ Platform
Prepared by
Kevin Munnelly
Business Unit Manager
Sr. Director, Genomics Products
617-908-5271
Email: kmunnelly@biotrove.com
Biotrove, Inc.
24 January 2007
BioTrove Confidential
2. BioTrove OpenArray™ Technology
BioTrove has developed the OpenArray™ platform based on through-hole technology, a
broadly applicable nanoliter fluidics technology for parallel and low-volume solution
phase reactions. The technology was invented at MIT by the founders of BioTrove and
exclusively licensed to BioTrove for all applications. OpenArray™ plates are coated
with hydrophilic coatings on the interior of each through hole and hydrophobic coatings
on the exterior of the through-holes. This enables OpenArray™ plates to hold solutions
in the open through-holes via capillary action. The OpenArray™ plate consists of 3072
through-holes that can be loaded with reagents to perform individual 33 nL reactions for
use in both real time qPCR applications as well as endpoint genotyping applications, such
as SNP typing and pathogen detection. The unique configuration of the through-holes
enables the researcher to interrogate a large number of nucleic acid samples against a
large number of assays in a flexible, configurable format. By altering the number of
assays or the number of samples the researcher can easily customize the OpenArray™ to
meet their changing needs. Researchers using this technology benefit from the
parallelism of microarrays and the data quality of solution phase reactions.
Overall Advantages of system
Throughput: generate thousands of data points
Low Volume: significant reagent savings
Flexible format and applications: ability to customize applications to specific
needs
Ease of use: add sample and enzymes and the system is ready
OpenArray™ Overview
BioTrove OpenArray™™ System. The BioTrove OpenArray™ is a high density,
through-hole, nanotiter plate used for conducting solution phase PCR
applications including SNP genotyping analyses and real time PCR in a micro
array format.
Key Features
• Microscope slide sized array of 3,072 through-holes (bottomless wells)
• Wells are preloaded with assay components (e.g., primer and probes)
• 33nL reactions
• Assays may be cycled on any flat block thermal cycler and read in BioTrove’s
imager, the NT-Imager™
BioTrove Confidential
3. • OpenArray™s are bar coded for identification and tracking, with
accompanying OpenArray™ data file descriptions
The OpenArray™ combines the
robustness of TaqMan® or SYBR
chemistry with the density of
arrays in BioTrove’s proprietary
nano-reaction wells. Precision
through-hole production and
proprietary coating technologies
enable capillary filling with <1%CV
BioTrove Confidential
4. High Throughput and flexibility
In addition to miniaturized reaction volumes and high throughput, the
OpenArray™ has a high degree of flexibility in both assay format and sample
throughput. This is due to a unique ability to put multiple samples onto the
OpenArray™.
• 64 specific assays are
applied in each subarray.
• A sample is applied to
each of 48 subarrays.
• A fully loaded
OpenArray™ plate may
contain 48 different
samples
Assay Loading- Pin Loading
Manufacturing Robot
Assays are pre-loaded onto BioTrove’s
OpenArray™ chip set using our
proprietary pin-loading manufacturing
robot.
A proprietary feature of this system is
a bar coded tracking of individual
OpenArray™ wells. This ensures
assays can be reliably traced back to
the 384 plates containing the master
assays as well as data from validation.
Biotrove’s high-throughput assay loading
system pre-loads up to hundreds of
OpenArrays with thousands of assays
ensuring availability of the content as
needed.
BioTrove Confidential
5. Array-in-Array™ Sample Loading
Each through-hole is filled The OpenArray™ is flooded with The OpenArray™ is inserted into a
with sample. sample loading fluid. case.
After loading, the samples are processed on the NT Cycler/Imager System.
• The BioTrove NT-Cycler is capable of processing
three OpenArrays at a time, which is up to 9216 PCR
reactions in a single run.
• The NT-Imager can detect SYBR® Green I, ROX,
FAM, and VIC®.
.
BioTrove Confidential
6. Life Sciences Research
The Openarray system is a fast path enabler for life science research as it
addresses the growing and critical need for biological validation and utilization of
genomic and genetic information archived in DNA sequence databases. Specific genetic
information encoded in a specimen’s DNA and RNA is analyzed by the OpenArray™ by
way of 3072 nanofluidic polymerase chain reactions (PCR) in a footprint the size of
microscope slide. Miniaturized, high throughput PCR gives researchers an unlimited
capability to ask accurate, precise and biologically pertinent questions by the “gold-
standard” PCR method to unlock the wealth of information embedded in the human
genome, accelerating the drive for discovery and implementation of novel medicines and
diagnostics.
The ability to perform hundreds of thousands of PCR based SNP reactions or real time
PCR reactions enable the researcher to discover or validate targets quickly and
efficiently. SNP experiments can be used for association studies, candidate gene studies,
model organism analysis, pharmacogenomic applications, loss of heterozygosity studies
and population based screening for epidemiology. Real time PCR can be used for
transcriptional profiling, methylation specific PCR studies, pharmacogenomic
applications, copy number polymorphisms and insertion deletion mapping.
Advantages:
Cost:
nL reactions save money on reagents
Significant FTE savings
Throughput:
24X the througput of most plate based systems
Flexibility:
Same equipment to run all applications
Time:
Large volume of Results in as little as three hours
Pathogen Surveillance and detection:
Comprehensive Antibody-antigen based schemes for detecting functional protein markers
can require hundreds of assays to detect multiple variants and multiple agents in the
presence of near-neighbor innocuous backgrounds.
The use of PCR assays in the detection microbial and viral pathogens have become
increasingly important and popular. As new pathogens are discovered, new strains are
created, or better assays become available, it is essential to have the flexibility to easily
change the assay content of a detection platform, rather than developing a new antibody
scheme to detect the new strain or mutation.
The OpenArray Platform delivers the speed, sensitivity and specificity of PCR detection,
which are required for these applications, in combination with flexible content and a
simple, high-throughput workflow. Each OpenArray plate can contain between 16 and
3072 assays and can be loaded with up to 144 samples. BioTrove proposes development
BioTrove Confidential
7. of technology to address objective of developing rapid, sensitive, cost-effective
diagnostics for simultaneously detecting multiple biological pathogens in a single assay,
whether viral or bacterial in nature.
Advantages
o Simultaneous Detection: Ability to identify strains and subtypes in a single
panel
o Sensitivity: reproducible detection for 100 copies. Single copy detection
proven.
o Flexibility in order to swap or add assays as needed
relevant for new strains or mutations
problematic for antigen tests (e.g. Antigen drift)
o Surge Capacity. An ability to analyze large numbers of samples as needed
o Results in hours, rather than days
o Option for quantification via real time PCR
Future Applications
BioTrove, Inc. intends to be the leader in molecular diagnostics by leveraging its core
OpenArray micro- and nanofluidic technologies to provide researchers and clinicians the
premier platform of solutions accelerating acquisition and translation of crucial biological
information for next-generation molecular diagnostics. Although the OpenArray is not
currently FDA validated, plans are in place to position BioTrove to reap the fruits of the
swelling life science research and development activities centered on the OpenArray™
nanofluidic system. As increasing numbers of researchers adopt the OpenArray™ as the
discovery and validation platform of choice, they will find a natural path into the MDx
marketplace for the biomarker panels discovered with the BioTrove technology is
through BioTrove. Our proprietary intellectual property position coupled with FDA-
approval of the OpenArray™ system will make BioTrove the preferred partner for
commercial delivery of the biomarker set to the MDx market.
BioTrove Confidential
8. Sample Data
SNP Genotyping
Heterozygotes
Homozygotes
NTCs
All Data at 1 ng per through-hole
unless otherwise specified
BioTrove Confidential