This document summarizes a presentation on high-performance cell-based assay and qPCR technologies for pathway-focused research. The presentation overview discusses QIAGEN's SABiosciences portfolio, PCR arrays, Cignal and Cignal Lenti pathway reporters, and provides a summary. PCR arrays allow analysis of mRNA expression of up to 84 genes related to biological pathways in a single experiment. Cignal reporter assays use dual-luciferase reporters to study 45 signal transduction pathways. Cignal Lenti reporters use lentiviral delivery of luciferase or GFP reporters to study pathways in difficult to transfect cells like stem cells or primary cells.
This document describes pathway-powered PCR arrays for gene expression analysis. It discusses:
- PCR arrays that analyze the expression of genes involved in biological pathways, covering sample prep through data analysis.
- Over 140 pathway-focused PCR arrays are available covering cancer, inflammation, neuroscience, and other areas.
- The PCR arrays allow analysis of mRNA expression from various sample types in a high-sensitivity and reproducible manner using real-time PCR instrumentation.
The document is a reference guide for pathway maps and related QIAGEN products. It includes a table of contents listing over 40 signaling pathways. For each pathway, it lists related RT2 Profiler PCR Arrays and Cignal Reporter Assay Kits from QIAGEN that can be used to study gene expression and transcription factor activity for that pathway. It also provides brief descriptions of the PCR array and reporter assay products and directs readers to QIAGEN websites for more information.
This document discusses using gene and miRNA expression profiling to develop biomarkers for monitoring genotoxicity. It describes:
1. Developing gene-based in vitro biomarkers for genotoxicity using RT2 Profiler PCR Arrays to analyze expression of DNA damage and p53 pathway genes in HepG2 cells exposed to genotoxic and non-genotoxic compounds. 11 genes were identified as classifiers.
2. Identifying miRNA-based in vivo biomarkers by profiling miRNA expression in mouse liver after exposure to the carcinogen ENU using miScript PCR Arrays. The mir-34 family showed temporal changes and clustering analysis identified differentially expressed miRNAs.
3. miRNA profiles have potential to serve as biomarkers for genotoxicity
Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...QIAGEN
miRNAs are small functional RNAs, which regulate gene expression post-transcriptionally. The miScript miRNA PCR Array System is a sensitive and reliable technology for detection of mature miRNAs in any laboratory. In this slideshow, the challenges of miRNA data analysis and solutions that the miScript miRNA PCR Arrays provide for researchers interested in identifying miRNA from cells, tissues and FFPE samples are described. You will also learn how to use our GeneGlobe Data Analysis Center to identify miRNAs that may be important in your favorite biological pathway or disease.
The document discusses using PCR arrays to profile gene expression and epigenetics. PCR arrays allow researchers to analyze expression of up to 84 genes related to a pathway or disease using real-time PCR. They include controls to check for genomic DNA contamination and assay performance. As an example, the document describes how a researcher could use a PCR array to compare gene expression between metastatic and non-metastatic breast tumor samples.
This document provides information about Norgen Biotek Corp., including their commitment to providing sample preparation kits and support services for nucleic acid purification, concentration, and stabilization for research and diagnostic applications. It specifically discusses their Rabies viral antigen detection kit, listing the kit catalog number, website for more information, and Norgen Biotek's corporate headquarters information and certifications. The document encourages contacting Norgen Biotek's technical support team with any questions.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cel...Qiagen - Egypt
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cell...QIAGEN
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
This document describes pathway-powered PCR arrays for gene expression analysis. It discusses:
- PCR arrays that analyze the expression of genes involved in biological pathways, covering sample prep through data analysis.
- Over 140 pathway-focused PCR arrays are available covering cancer, inflammation, neuroscience, and other areas.
- The PCR arrays allow analysis of mRNA expression from various sample types in a high-sensitivity and reproducible manner using real-time PCR instrumentation.
The document is a reference guide for pathway maps and related QIAGEN products. It includes a table of contents listing over 40 signaling pathways. For each pathway, it lists related RT2 Profiler PCR Arrays and Cignal Reporter Assay Kits from QIAGEN that can be used to study gene expression and transcription factor activity for that pathway. It also provides brief descriptions of the PCR array and reporter assay products and directs readers to QIAGEN websites for more information.
This document discusses using gene and miRNA expression profiling to develop biomarkers for monitoring genotoxicity. It describes:
1. Developing gene-based in vitro biomarkers for genotoxicity using RT2 Profiler PCR Arrays to analyze expression of DNA damage and p53 pathway genes in HepG2 cells exposed to genotoxic and non-genotoxic compounds. 11 genes were identified as classifiers.
2. Identifying miRNA-based in vivo biomarkers by profiling miRNA expression in mouse liver after exposure to the carcinogen ENU using miScript PCR Arrays. The mir-34 family showed temporal changes and clustering analysis identified differentially expressed miRNAs.
3. miRNA profiles have potential to serve as biomarkers for genotoxicity
Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...QIAGEN
miRNAs are small functional RNAs, which regulate gene expression post-transcriptionally. The miScript miRNA PCR Array System is a sensitive and reliable technology for detection of mature miRNAs in any laboratory. In this slideshow, the challenges of miRNA data analysis and solutions that the miScript miRNA PCR Arrays provide for researchers interested in identifying miRNA from cells, tissues and FFPE samples are described. You will also learn how to use our GeneGlobe Data Analysis Center to identify miRNAs that may be important in your favorite biological pathway or disease.
The document discusses using PCR arrays to profile gene expression and epigenetics. PCR arrays allow researchers to analyze expression of up to 84 genes related to a pathway or disease using real-time PCR. They include controls to check for genomic DNA contamination and assay performance. As an example, the document describes how a researcher could use a PCR array to compare gene expression between metastatic and non-metastatic breast tumor samples.
This document provides information about Norgen Biotek Corp., including their commitment to providing sample preparation kits and support services for nucleic acid purification, concentration, and stabilization for research and diagnostic applications. It specifically discusses their Rabies viral antigen detection kit, listing the kit catalog number, website for more information, and Norgen Biotek's corporate headquarters information and certifications. The document encourages contacting Norgen Biotek's technical support team with any questions.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cel...Qiagen - Egypt
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cell...QIAGEN
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
RT2 Profiler PCR Arrays allow researchers to analyze gene expression profiles for focused panels of genes involved in biological pathways or disease states. The arrays provide laboratory-verified gene assays, integrated controls, and free data analysis software to generate a gene expression profile from a sample in less than 3 hours. Popular arrays analyze pathways such as extracellular matrix and adhesion molecules, WNT signaling, and cancer-related genes. The complete workflow begins with sample preparation and ends with data interpretation and publication 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.
Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. PCR was invented in 1984 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to much of genetic testing including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory and clinical laboratory research for a broad variety of applications including biomedical research and criminal forensics
The document summarizes three studies using RT2 Profiler PCR Arrays to examine gene expression changes in toxicology, oncology, and immunology research. In toxicology, the arrays identified distinct gene expression profiles for three drugs (troglitazone, pioglitazone, rosiglitazone) in liver cells, suggesting different mechanisms for their liver toxicity effects. In oncology, arrays revealed gene expression differences between breast tumor and normal tissue. In immunology, array results correlated well with measured cytokine protein levels between stimulated and unstimulated immune cells.
The document discusses Cignal Reporter Assays, which are cell-based assays for analyzing gene expression and signaling pathways. The assays use dual-luciferase technology and transcription factor-targeted response elements to provide sensitive and reproducible measurements of 45 signaling pathways. Key advantages of the assays include minimizing experimental variability through dual-luciferase normalization, increasing signal-to-noise ratio using destabilized and codon-optimized luciferase, and maximizing response using optimized transcriptional response elements tailored to each pathway. The assays are available in multiple formats including plasmid, lentiviral, luciferase and GFP, making them suitable for a variety of experimental systems and applications.
This document discusses using qPCR arrays to screen and validate induced pluripotent stem cells (iPSCs). It describes how iPSCs are created by reprogramming somatic cells, and the need to validate pluripotency. Validation methods discussed include checking for pluripotency biomarkers using qPCR arrays, which allow screening multiple genes from multiple samples simultaneously. The document provides an example of a qBiomarker iPSC screening PCR array, which contains assays for 8 predictive pluripotency biomarkers, a normalization gene, and control wells to screen 8 samples per plate for pluripotent stem cell characterization.
The document provides an overview of PCR array technology for gene expression analysis from QIAGEN. It describes how RT2 Profiler PCR arrays work to simultaneously analyze the expression of multiple pathway-focused genes. Popular array types are listed, including inflammatory cytokines and receptors, oxidative stress, and stem cell arrays. The document highlights the simplicity, performance, and relevance of PCR arrays for expression profiling. It also provides examples of array applications in angiogenesis, cancer biomarker discovery, immune response, and determining drug toxicity.
This document provides an overview of RT2 Profiler PCR Arrays from SABiosciences, which allow for gene expression analysis from small samples and FFPE samples. The document discusses how PCR Arrays work using SABiosciences' PreAMP technology to increase sensitivity for samples containing as little as 1-100ng of RNA. It also reviews the performance data demonstrating the ability of PreAMP to detect more genes and shift genes with high Ct values into the detectable range. Finally, it highlights the complete PCR Array system from SABiosciences which provides optimized kits, controls, and software for reliable gene expression analysis from sample to results in about 3 hours.
PCR - From Setup to Cleanup: A Beginner`s Guide with Useful Tips and Tricks -...QIAGEN
This End-Point PCR Beginner´s Guide will not only give you a comprehensive overview of tools and techniques to help you to get the most out of your samples, but also give you information on dedicated solutions and complete workflows on multiplex PCR and PCR fragment analysis.
This document provides information about qBiomarker somatic mutation PCR arrays for cancer mutation analysis. It discusses how the arrays can detect mutations in key cancer genes and pathways. The document outlines the workflow, which involves using quantitative PCR to detect mutations in DNA samples. Data is analyzed by comparing Ct values between mutation assays and controls to identify which samples contain mutations. The document provides examples of this analysis method using lung and colon cancer cell line and patient samples.
A next generation sequencing based sample-to-result pharmacogenomics research...Thermo Fisher Scientific
Pharmacogenomics (PGx) is the study of genetic variations in terms of their response to drugs. Variations in gene sequence or copy numbers may result in complete loss of function, partial decrease or increase in enzyme activity, or an altered affinity for substrates, which may in turn significantly impact drug efficacy. PGx studies are becoming increasingly important for precision medicine. We have developed a next generation sequencing (NGS) PGx research solution with increased flexibility on the assay targets and combined detection of SNP/INDEL genotyping and CNV using Ion AmpliSeq™ technology for low to medium throughput laboratories. With this highly multiplexed PGx research panel we can profile a set of 136 genetic markers in 40 known PGx related genes (Table 1) and determine CYP2D6 copy number variation (CNV, Figure 1) in a single reaction using Ion Torrent™ semiconductor sequencing.
10 Tips to maximize your Real Time PCR Success - Download the Technical NoteQIAGEN
This document provides 10 tips for maximizing success with real-time PCR. The tips include using high-quality nucleic acid templates, determining template concentration and purity, checking storage conditions, using the optimal template amount, determining reaction efficiency for each primer pair, properly storing primers and probes, preventing contamination, thoroughly mixing reaction components, performing necessary control reactions, and double checking cycler settings.
SARS-CoV-2 (COVID-19) is the virus responsible for respiratory disease caused by a novel (new) coronavirus that was first detected in Wuhan City, Hubei Province, China, later causing a global pandemic.
The virus is contagious and can be spread from humans to humans primarily through the exchange of mucus droplets that are expelled through sneezes or coughs.
The SARS-CoV-2 is a severe acute respiratory syndrome coronavirus. This outbreak is an important reminder that the global community must strengthen national and international programs for detection and response to future disease outbreaks.
This document provides an overview of RNA interference (RNAi) technology and its applications in high-throughput screening. It discusses the RNAi pathway and how siRNAs can be used to silence gene expression. The document outlines some challenges of RNAi screening including off-target effects and highlights the importance of validation. It also promotes QIAGEN's siRNA design tools and libraries for optimizing RNAi experiments and minimizing false positives and negatives in high-throughput screens.
This document describes a kit for detecting the human pathogen Mycobacterium tuberculosis using PCR. It discusses how the kit allows for isolation of DNA from samples using a spin column method. It then can detect M. tuberculosis through amplification of a region of its genome using provided master mixes and controls. The kit is designed for testing 24 samples at a time and provides high sensitivity and specificity for detection of this important pathogen.
Multicopy reference assay (MRef) — a superior normalizer of sample input in D...QIAGEN
Copy number variations (CNVs) and alterations (CNAs) are a source of genetic diversity in humans and are often pathogenic. Numerous CNVs and CNAs are being identified with various genome analysis platforms, including array comparative genomic hybridization (aCGH), single nucleotide polymorphism (SNP) genotyping platforms, and next-generation sequencing. Independent verification of copy number changes is a critical step. Quantitative real-time PCR (qPCR) is a classic method to verify microarray copy number findings. Traditional copy number assays that use qPCR typically rely on a putative single-copy gene reference assay (e.g., RNase P or TERT) to normalize the DNA input for downstream ΔΔCT-based copy number calculation for comparison to a reference genome. When applied to cancer samples, these single-copy reference assays may no longer be a reliable indicator of DNA input due to the presence of complex chromosome composition (both in chromosome number and structure). To meet the need for an accurate DNA input normalizer, especially for heterogeneous tumor samples, QIAGEN developed a multicopy reference (MRef) assay for real-time PCR copy number analysis. This assay, in conjunction with QIAGEN’s greater than 10 million genomewide copy number assays and pathway- and disease-focused copy number PCR arrays (Figure 1), provides a successful solution for copy number analysis. This article will address the assay design considerations, development, and performance of this multicopy reference (MRef) assay.
Learn about the power of LNA (Locked Nucleic Acid) technology and QIAGEN's LNA enhanced product portfolio for RNA and DNA research. Download the slide deck!
Automated DNA extraction from FFPE tissue using a xylene free deparaffinizati...QIAGEN
Formalin-fixed paraffin-embedded (FFPE) tissue samples are routinely used for immunohistochemistry and molecular analysis in cancer research. However, many methods for DNA extraction from FFPE tissue sections are manual procedures that are not standardized, time consuming and often involve the use of hazardous materials like xylene. Recently we introduced an automated solution for the DNA extraction from FFPE tissue using the QIAsymphony SP instrument in combination with the QIAsymphony DNA Mini kit.
PCR Array Data Analysis Tutorial: qPCR Technology Webinar Series Part 3QIAGEN
This webinar presentation provides an overview and tutorial on analyzing data from RT2 Profiler PCR Array experiments. It discusses organizing raw Ct value data, performing ΔCt and ΔΔCt calculations to analyze gene expression changes between sample groups, and using the GeneGlobe Data Analysis Center web portal to analyze the data. The webinar highlights new features of the Data Analysis Center including improved data visualization and an upgraded sample manager. It emphasizes following the standard protocol for setting baselines and thresholds when analyzing PCR array data.
Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. PCR was invented in 1984 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to much of genetic testing including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory and clinical laboratory research for a broad variety of applications including biomedical research and criminal forensics.
Cell based assays presentation V2_03_2012Pete Shuster
This document provides an executive overview of a company called Neuromics/Vitro Biopharma that develops pre-clinical tools for drug discovery using human stem cell-derived cell systems. The company offers physiologically relevant human cells and cellular systems to enable better in vitro screening and target identification, reducing animal models and shortening development timelines. Key offerings include human stem cell-derived neuronal cells, glial cells, immune cells and other cell types, specialized media, transfection reagents, markers and labeling technologies. The company aims to improve early drug discovery through more predictive human cell-based assays.
RT2 Profiler PCR Arrays allow researchers to analyze gene expression profiles for focused panels of genes involved in biological pathways or disease states. The arrays provide laboratory-verified gene assays, integrated controls, and free data analysis software to generate a gene expression profile from a sample in less than 3 hours. Popular arrays analyze pathways such as extracellular matrix and adhesion molecules, WNT signaling, and cancer-related genes. The complete workflow begins with sample preparation and ends with data interpretation and publication 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.
Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. PCR was invented in 1984 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to much of genetic testing including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory and clinical laboratory research for a broad variety of applications including biomedical research and criminal forensics
The document summarizes three studies using RT2 Profiler PCR Arrays to examine gene expression changes in toxicology, oncology, and immunology research. In toxicology, the arrays identified distinct gene expression profiles for three drugs (troglitazone, pioglitazone, rosiglitazone) in liver cells, suggesting different mechanisms for their liver toxicity effects. In oncology, arrays revealed gene expression differences between breast tumor and normal tissue. In immunology, array results correlated well with measured cytokine protein levels between stimulated and unstimulated immune cells.
The document discusses Cignal Reporter Assays, which are cell-based assays for analyzing gene expression and signaling pathways. The assays use dual-luciferase technology and transcription factor-targeted response elements to provide sensitive and reproducible measurements of 45 signaling pathways. Key advantages of the assays include minimizing experimental variability through dual-luciferase normalization, increasing signal-to-noise ratio using destabilized and codon-optimized luciferase, and maximizing response using optimized transcriptional response elements tailored to each pathway. The assays are available in multiple formats including plasmid, lentiviral, luciferase and GFP, making them suitable for a variety of experimental systems and applications.
This document discusses using qPCR arrays to screen and validate induced pluripotent stem cells (iPSCs). It describes how iPSCs are created by reprogramming somatic cells, and the need to validate pluripotency. Validation methods discussed include checking for pluripotency biomarkers using qPCR arrays, which allow screening multiple genes from multiple samples simultaneously. The document provides an example of a qBiomarker iPSC screening PCR array, which contains assays for 8 predictive pluripotency biomarkers, a normalization gene, and control wells to screen 8 samples per plate for pluripotent stem cell characterization.
The document provides an overview of PCR array technology for gene expression analysis from QIAGEN. It describes how RT2 Profiler PCR arrays work to simultaneously analyze the expression of multiple pathway-focused genes. Popular array types are listed, including inflammatory cytokines and receptors, oxidative stress, and stem cell arrays. The document highlights the simplicity, performance, and relevance of PCR arrays for expression profiling. It also provides examples of array applications in angiogenesis, cancer biomarker discovery, immune response, and determining drug toxicity.
This document provides an overview of RT2 Profiler PCR Arrays from SABiosciences, which allow for gene expression analysis from small samples and FFPE samples. The document discusses how PCR Arrays work using SABiosciences' PreAMP technology to increase sensitivity for samples containing as little as 1-100ng of RNA. It also reviews the performance data demonstrating the ability of PreAMP to detect more genes and shift genes with high Ct values into the detectable range. Finally, it highlights the complete PCR Array system from SABiosciences which provides optimized kits, controls, and software for reliable gene expression analysis from sample to results in about 3 hours.
PCR - From Setup to Cleanup: A Beginner`s Guide with Useful Tips and Tricks -...QIAGEN
This End-Point PCR Beginner´s Guide will not only give you a comprehensive overview of tools and techniques to help you to get the most out of your samples, but also give you information on dedicated solutions and complete workflows on multiplex PCR and PCR fragment analysis.
This document provides information about qBiomarker somatic mutation PCR arrays for cancer mutation analysis. It discusses how the arrays can detect mutations in key cancer genes and pathways. The document outlines the workflow, which involves using quantitative PCR to detect mutations in DNA samples. Data is analyzed by comparing Ct values between mutation assays and controls to identify which samples contain mutations. The document provides examples of this analysis method using lung and colon cancer cell line and patient samples.
A next generation sequencing based sample-to-result pharmacogenomics research...Thermo Fisher Scientific
Pharmacogenomics (PGx) is the study of genetic variations in terms of their response to drugs. Variations in gene sequence or copy numbers may result in complete loss of function, partial decrease or increase in enzyme activity, or an altered affinity for substrates, which may in turn significantly impact drug efficacy. PGx studies are becoming increasingly important for precision medicine. We have developed a next generation sequencing (NGS) PGx research solution with increased flexibility on the assay targets and combined detection of SNP/INDEL genotyping and CNV using Ion AmpliSeq™ technology for low to medium throughput laboratories. With this highly multiplexed PGx research panel we can profile a set of 136 genetic markers in 40 known PGx related genes (Table 1) and determine CYP2D6 copy number variation (CNV, Figure 1) in a single reaction using Ion Torrent™ semiconductor sequencing.
10 Tips to maximize your Real Time PCR Success - Download the Technical NoteQIAGEN
This document provides 10 tips for maximizing success with real-time PCR. The tips include using high-quality nucleic acid templates, determining template concentration and purity, checking storage conditions, using the optimal template amount, determining reaction efficiency for each primer pair, properly storing primers and probes, preventing contamination, thoroughly mixing reaction components, performing necessary control reactions, and double checking cycler settings.
SARS-CoV-2 (COVID-19) is the virus responsible for respiratory disease caused by a novel (new) coronavirus that was first detected in Wuhan City, Hubei Province, China, later causing a global pandemic.
The virus is contagious and can be spread from humans to humans primarily through the exchange of mucus droplets that are expelled through sneezes or coughs.
The SARS-CoV-2 is a severe acute respiratory syndrome coronavirus. This outbreak is an important reminder that the global community must strengthen national and international programs for detection and response to future disease outbreaks.
This document provides an overview of RNA interference (RNAi) technology and its applications in high-throughput screening. It discusses the RNAi pathway and how siRNAs can be used to silence gene expression. The document outlines some challenges of RNAi screening including off-target effects and highlights the importance of validation. It also promotes QIAGEN's siRNA design tools and libraries for optimizing RNAi experiments and minimizing false positives and negatives in high-throughput screens.
This document describes a kit for detecting the human pathogen Mycobacterium tuberculosis using PCR. It discusses how the kit allows for isolation of DNA from samples using a spin column method. It then can detect M. tuberculosis through amplification of a region of its genome using provided master mixes and controls. The kit is designed for testing 24 samples at a time and provides high sensitivity and specificity for detection of this important pathogen.
Multicopy reference assay (MRef) — a superior normalizer of sample input in D...QIAGEN
Copy number variations (CNVs) and alterations (CNAs) are a source of genetic diversity in humans and are often pathogenic. Numerous CNVs and CNAs are being identified with various genome analysis platforms, including array comparative genomic hybridization (aCGH), single nucleotide polymorphism (SNP) genotyping platforms, and next-generation sequencing. Independent verification of copy number changes is a critical step. Quantitative real-time PCR (qPCR) is a classic method to verify microarray copy number findings. Traditional copy number assays that use qPCR typically rely on a putative single-copy gene reference assay (e.g., RNase P or TERT) to normalize the DNA input for downstream ΔΔCT-based copy number calculation for comparison to a reference genome. When applied to cancer samples, these single-copy reference assays may no longer be a reliable indicator of DNA input due to the presence of complex chromosome composition (both in chromosome number and structure). To meet the need for an accurate DNA input normalizer, especially for heterogeneous tumor samples, QIAGEN developed a multicopy reference (MRef) assay for real-time PCR copy number analysis. This assay, in conjunction with QIAGEN’s greater than 10 million genomewide copy number assays and pathway- and disease-focused copy number PCR arrays (Figure 1), provides a successful solution for copy number analysis. This article will address the assay design considerations, development, and performance of this multicopy reference (MRef) assay.
Learn about the power of LNA (Locked Nucleic Acid) technology and QIAGEN's LNA enhanced product portfolio for RNA and DNA research. Download the slide deck!
Automated DNA extraction from FFPE tissue using a xylene free deparaffinizati...QIAGEN
Formalin-fixed paraffin-embedded (FFPE) tissue samples are routinely used for immunohistochemistry and molecular analysis in cancer research. However, many methods for DNA extraction from FFPE tissue sections are manual procedures that are not standardized, time consuming and often involve the use of hazardous materials like xylene. Recently we introduced an automated solution for the DNA extraction from FFPE tissue using the QIAsymphony SP instrument in combination with the QIAsymphony DNA Mini kit.
PCR Array Data Analysis Tutorial: qPCR Technology Webinar Series Part 3QIAGEN
This webinar presentation provides an overview and tutorial on analyzing data from RT2 Profiler PCR Array experiments. It discusses organizing raw Ct value data, performing ΔCt and ΔΔCt calculations to analyze gene expression changes between sample groups, and using the GeneGlobe Data Analysis Center web portal to analyze the data. The webinar highlights new features of the Data Analysis Center including improved data visualization and an upgraded sample manager. It emphasizes following the standard protocol for setting baselines and thresholds when analyzing PCR array data.
Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. PCR was invented in 1984 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to much of genetic testing including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory and clinical laboratory research for a broad variety of applications including biomedical research and criminal forensics.
Cell based assays presentation V2_03_2012Pete Shuster
This document provides an executive overview of a company called Neuromics/Vitro Biopharma that develops pre-clinical tools for drug discovery using human stem cell-derived cell systems. The company offers physiologically relevant human cells and cellular systems to enable better in vitro screening and target identification, reducing animal models and shortening development timelines. Key offerings include human stem cell-derived neuronal cells, glial cells, immune cells and other cell types, specialized media, transfection reagents, markers and labeling technologies. The company aims to improve early drug discovery through more predictive human cell-based assays.
Dr. Alastair Brown Dr. Rochdi Bouhelal 15:00 - 15:30 Coffee & Networking Break
Associate Principal Scientist Senior Investigator
AstraZeneca Novartis
15:30 - 17:00 Panel Discussion & Q&A
Panelist: Dr. Magalie Rocheville Dr. Nick Thomas 17:00 - 17:30 Closing Remarks & Networking Drinks
Investigator, Molecular Discovery Research Principal Scientist
Glax
The MTT assay is a quantitative method to measure cell growth and viability. It works by using the yellow tetrazolium dye MTT, which is reduced to purple formazan in the mitochondria of living cells. The amount of formazan produced is proportional to the number of viable cells and can be measured spectrophotometrically. The MTT assay is important for measuring cellular proliferation in response to external factors and has applications in testing drug sensitivity, cytotoxicity, and cell responses to growth factors.
An assay uses biological testing to measure substances like drugs. There are chemical and biological (bio) assays. Bioassays measure effects on living organisms and are used when chemical methods can't identify or quantify a substance. They can measure potency but are less precise, costly, and time-consuming than chemical assays. Bioassays involve exposing test animals to samples and standards to compare biological effects. They help standardize substances and determine specific effects but response can vary between individuals and species.
An Over view on Bioassay, structure & principles, types & methods of bioassay. Also mention of other assay's like biotechnology, microbio assay, immunoassay etc.
ADCC Reporter Bioassay - V and F Variants: Novel, Bioluminescent Cell-Based A...Neal Cosby
The ADCC Reporter Bioassay from Promega is now available in both V158 and F158 variant formats. Use this functional, sister bioassay approach to better characterize Ab drugs with MOA directed through FcgammaRIIIa (CD16a) receptor. Not yet familiar with this novel bioassay that is becoming the industry standard? This slidedoc introduces the reporter-based ADCC technology. Contact me for any questions.
The document describes Cignal Reporter Assays from SABiosciences that enable simple and robust analysis of signal transduction pathways. The assays utilize dual-luciferase reporters containing optimized transcriptional regulatory elements and luciferase variants to provide high sensitivity and low variability. The assays allow monitoring of 29 pathways and are available in different formats for various cell types and applications like RNAi and small molecule screening.
BioMAP<sup>®</sup> Primary Human Cell-Based Systems for Drug DiscoveryBioMAP® Systems
The document discusses BioMAP, a platform using primary human cell-based disease models to characterize compounds and discover their mechanisms of action and toxicity. It can assess over 2000 compounds across diverse pathways and targets. BioMAP generates biological profiles for compounds and uses these to classify compounds by similarity of mechanism. It has been used in collaborations to efficiently profile EPA ToxCast compounds and identify unexpected targets. The platform bridges molecular and cellular data to help validate targets and indications and connect to in vivo studies.
1. Addex Pharmaceuticals has developed novel assays to improve GPCR and non-GPCR target screening for allosteric modulator discovery.
2. Their cAMP Phoenyx biosensor provides a dynamic, real-time measurement of receptor activation without altering homeostasis.
3. For GPCRs, the ADX Tags Series 1 assay monitors receptor activation by tagging receptors and binding partners to detect interactions.
4. For non-GPCRs, the Accessory Protein Relocalization Assay detects receptor activation by visualizing accessory protein recruitment.
This document provides a list of 10 core assays for testing compounds that modulate the immune system. The assays measure things like cell proliferation, nitric oxide release from macrophages, and cytokine release from splenocytes or human PBMCs in response to test compounds. Each assay is described in terms of the test model, turnaround time, minimum compound requirement, and standard reporting format. The assays will help optimize leads for anti-inflammatory, pro-inflammatory, or other immunomodulatory activities.
This document discusses bioassay development for drug discovery. It covers in vitro and cell-based bioassays, as well as the molecular biology techniques used to develop these assays such as cloning DNA into plasmids, propagating plasmids in bacteria, purifying plasmid DNA, sequencing DNA, and expressing proteins in bacteria and mammalian cells through techniques like transfection. Recombinant protein expression and purification using affinity tags is also summarized.
―Study of Ligand Based Virtual Screening Tools in Computer Aided Drug Designi...iosrjce
Insilico potential drug target identification involves chemical compounds for inhibiting or promoting
chemical reactions in living organism computational methods are needed for screening through large database
of these to identify a inhibitor for receptor 0ral Multi-AGC Kinase was employed for docking.We investigated
the detailed pharmacology and antitumour activity of the novel clinical drugs and natural ligand. It is
associated with Oral Multi-AGC kinase protein. The various ZINC analogs on basis of 99%, 95%, 90%
similarity for best docking results with protein for predicting a ZINC analog which can be identified under the
category of becoming a potential drug candidate in future. The best mol dock score were for ZINC analog ZINC
ID 72131268 for Irinotecan is -169.087 kcl/mol, ZINC ID 04166028 for Teniposide is -178.235 kcl/mol, ZINC
ID 30731084 for Topotecan is -166.939 kcl/mol and ZINC ID 00899824 for Curcumin is -141.537 kcl/mol.
The two parameter for toxicity properties i.e. Oral LD50 and Mutagenicity were calculated. Oral LD50 and
Mutagenicity values are found.
Rapid diagnostic tests (RIDTs) can diagnose influenza quickly but have lower accuracy than polymerase chain reaction (PCR) tests, which take 1-10 days for results but are more sensitive. A study found RIDTs have higher accuracy in children than adults. While RIDTs are useful for influenza treatment, they cannot rule out influenza on their own. Additionally, a new PCR-based technique can identify sloth species using mitochondrial DNA, allowing for more effective conservation management.
Ligand binding involves a reversible reaction where a ligand (L) binds to a macromolecule or receptor (M) to form a ligand-receptor complex (ML). The equilibrium dissociation constant (KD) describes the affinity of the ligand for the receptor, with lower KD values indicating tighter binding. The fractional saturation (Y) represents the fraction of receptor occupied by ligand and depends on the ligand concentration and KD. At ligand concentrations much greater than KD, saturation is reached where all receptors are occupied. At ligand levels below KD, binding follows linear kinetics where Y is directly proportional to ligand concentration divided by KD.
The document discusses the increasing role of PCR in medical diagnostics. It begins by explaining what PCR is and how it works to amplify DNA segments. It then describes the three main uses of PCR in clinical settings: 1) to detect genetic mutations, 2) to detect microbial genes in samples, and 3) to amplify human DNA from limited samples. The rest of the document provides examples of how PCR has improved the diagnosis of genetic diseases and infections compared to previous methods. It concludes that while PCR has limitations, it has proven more sensitive than gold standard tests in many cases by overcoming barriers of other diagnostic techniques.
PCR (polymerase chain reaction) is used to create millions of copies of DNA fragments through repeated cycles of heating and cooling, allowing DNA to be amplified. The document discusses several applications of PCR including genetic engineering, bioremediation, detecting genetically modified organisms, diagnosing genetic diseases and infectious diseases, forensic analysis, evolutionary studies, and medical research. Specifically, PCR can be used to insert cloned DNA fragments into organisms, detect mutations, screen for genetic diseases before birth, detect pathogens in water supplies, and identify criminals through DNA fingerprinting.
This document discusses primer design concepts and applications of real-time PCR. It covers guidelines for optimal primer design such as length, GC content, and melting temperature. Longer primers are more specific but risk secondary structure formation. Primer dimers can decrease efficiency. Real-time PCR has applications in biomedical research, genetic disease diagnosis, cancer research, and forensics. It allows monitoring amplification in real-time and precise quantification of DNA or RNA.
This slidedeck presents a simple and accurate real-time PCR system for relevant biological pathway- and disease-focused mRNA and long noncoding RNA (lncRNA) expression profiling. Learn about the stringent performance built into the technology to ensure its sensitivity, specificity, reproducibility and reliability. Application examples are also presented.
Technical Guide to Qiagen PCR Arrays - Download the GuideQIAGEN
Total RNA discovery with RT2 and miScript PCR Arrays : Explore the RNA universe - Whatever your destination within the RNA universe, QIAGEN will help you get there. The miRNeasy kits deliver pure, high-quality total RNA from a broad range of samples. The RT2 and miScript PCR arrays are a complete solution both for focused analysis of gene and microRNA expression and for validation of microarray and RNA sequencing experiments. Together with the powerful analytics tools of GeneGlobe® and QIAGEN Ingenuity® Pathway Analysis, these products give you a smooth path from your sample to high-quality results.
The document describes miScript miRNA PCR Arrays for analyzing miRNA expression patterns. It discusses miRNA biogenesis and function, and how the miScript system allows for genome-wide and pathway-focused miRNA analysis using a qPCR-based approach. The miScript arrays offer high reproducibility, sensitivity, and the ability to discover cancer-related and developmentally regulated miRNAs. They can be used to screen focused miRNA panels or conduct genome-wide screens to discover novel miRNA roles.
This document describes SureFIND Transcriptome PCR Arrays, which are ready-to-use cDNA panels that can identify the miRNAs, pathways, or transcription factors that regulate gene expression. Each array contains cDNA from cells treated with different factors, such as miRNA mimics or pathway inhibitors. The document outlines an example where a Transcriptome PCR Array identified three miRNAs - miR-193b, miR-138, and miR-373 - that regulate the INPPL1 gene. Users are encouraged to validate top hits from the arrays.
Please note: This presentation accompanies a recorded webinar at:
https://www1.gotomeeting.com/register/347794241
Biomarkers for studying gene regulation and cell function can be efficiently analyzed by multiplexed methods. Dr. Jim Lazar from OriGene Technologies will provide an overview of four different but related detection technologies that can be used to analyze genetic variants, microRNA expression, transcription factor binding, and protein expression on the Luminex xMAP platform. OriGene’s broad panel of assays and tools for discovery, analysis and validation of multiple classes of important biomarkers will allow researcher to develop more accurate descriptions of biologically complex systems.
This technical article describes three case studies using RT2 Profiler PCR Arrays to analyze gene expression changes in different research areas: toxicology, oncology, and immunology. In the toxicology study, liver cells were treated with three drugs known to cause liver toxicity and the PCR Array identified distinct gene expression patterns for each drug, suggesting different mechanisms of toxicity. In the oncology study, gene expression in breast tumor samples was compared to normal tissue and a common set of upregulated genes was discovered in two independent tumor samples. In the immunology study, stimulated immune cells showed good correlation between cytokine gene and protein expression levels. The article concludes the PCR Array System is a reliable and accurate tool for pathway-focused gene expression profiling across
This document discusses microRNAs (miRNAs) and methods for studying their function and regulation of genes. It describes:
1) What miRNAs are, how they work by incorporating into the RISC complex and repressing target mRNAs through translational repression or degradation.
2) Techniques for manipulating miRNAs in cell lines using reporter assays, mimics, inhibitors and target protectors to study their effects on genes.
3) How to screen for miRNAs that regulate a target gene using ready-made cDNA panels and quantitative PCR. Several examples are provided of identifying miRNAs that regulate important cancer genes.
RT2 Profiler PCR Arrays allow researchers to analyze gene expression in biological pathways or disease states using real-time PCR. The document discusses:
1. PCR Arrays focus on profiling genes relevant to specific pathways or disease states. They provide a simple, reproducible, and sensitive way to simultaneously profile expression of many genes related to a pathway.
2. Examples are provided demonstrating how PCR Arrays have been used in cancer research to discover breast cancer biomarkers, in immunology research to monitor cytokine induction, and in toxicity research to determine drug toxicity profiles.
3. Key advantages of PCR Arrays are highlighted, including their simplicity, performance, relevance to specific pathways, and ability to analyze gene expression from small amounts
This document discusses new assays for microRNA (miRNA) research, including isolation, expression analysis, and functional analysis. It describes miRNA isolation kits that can purify miRNAs from various sample types. For expression analysis, it highlights real-time PCR-based miRNA assays, including miRNA PCR arrays that can profile hundreds of miRNAs simultaneously. It also discusses tools for identifying miRNA targets and analyzing miRNA function, such as miRNA mimics and inhibitors. Examples are given of how these assays have been used to study miRNAs in cancer and other diseases.
Targeted RNAseq for Gene Expression Using Unique Molecular Indexes (UMIs): In...QIAGEN
Traditional RNA sequencing (RNA-Seq) is a powerful tool for expression profiling, but is hindered by PCR amplification bias and inaccuracy at low expressing genes. QIAseq RNA is a flexible and precise tool developed for mitigating these complications, allowing digital gene expression analysis. This in-depth webinar will cover sample requirements, experimental design, NGS platform-specific challenges and workflow for gene enrichment, library prep and sequencing. The applications of QIASeq RNA Panels in cancer research, stem cell differentiation and elucidating the effects small molecules on signaling pathways will be highlighted.
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...QIAGEN
This document discusses a 4-part webinar series on microRNA (miRNA) research presented by QIAGEN. Part 1 will cover miRNA profiling from biofluids, part 2 will discuss challenges in miRNA research, part 3 will focus on advanced miRNA expression analysis, and part 4 will analyze functional analysis of miRNA. The document provides background on miRNAs and their role in gene expression and disease. It also describes QIAGEN products and solutions for miRNA sample preparation, real-time PCR, data analysis, and functional validation to help researchers overcome challenges in miRNA analysis.
Massively Parallel Sequencing - integrating the Ion PGM™ sequencer into your ...Thermo Fisher Scientific
This document summarizes the integration of massively parallel sequencing (MPS) using the Ion PGMTM sequencer into a forensic laboratory. The project aims to begin transforming STR profiling to genomic technologies, add additional SNP markers in a single workflow, and enable non-human DNA testing. Initial results show sequencing of amplified STR products is possible but alignment is challenging. A custom panel of 280 targets including STRs, SNPs, and amelogenin was also tested with most targets detected across samples. Ongoing work focuses on improving sensitivity, reproducibility, and analyzing mixed samples. Implementation of MPS as a routine forensic service is estimated within 3-5 years.
The document describes miScript miRNA PCR Arrays, which enable comprehensive profiling of miRNAs for disease research and biomarker discovery. The arrays use a validated PCR technique to quantify miRNA expression levels from tissue samples. They are available in customizable panels focused on specific biological pathways, diseases, or the entire miRNome. The workflow involves isolating miRNA from samples, converting it to cDNA, and running real-time PCR on the array to obtain expression data for targeted miRNAs. The technique provides sensitive and reproducible miRNA profiling to explore their roles in biological contexts and diseases.
Total RNA Discovery for RNA Biomarker Development WebinarQIAGEN
Precision medicine offers to transform patient care by targeting treatment to those with most to gain. To date the most significant advances have been at the level of DNA, for example, the use of somatic DNA alterations as diagnostic indicators of disease and for prediction of pharmacodynamic response. Development of RNA expression signatures as biomarkers has been more problematic. While RNA expression analysis has yielded valuable insights into the biological mechanisms of disease, RNA is a more unstable molecule than DNA, and more easily damaged or degraded during sample collection and isolation. In addition, RNA levels are inherently dynamic and gene expression signatures are extraordinarily complex. Recently, much progress has been made in identifying key changes in gene expression in cancer and other diseases, as well as identifying expression signatures in circulating nucleic acid that have the potential to be developed into diagnostic and prognostic indicators.
The document describes miScript miRNA PCR Arrays, which enable comprehensive profiling of miRNAs for disease research and biomarker discovery. The arrays contain extensively verified assays for miRNAs related to biological pathways and diseases. The miScript PCR system provides sensitive and reproducible quantification of miRNA expression. It allows isolation of miRNA from samples, conversion to cDNA, and real-time PCR profiling of miRNA expression across pathway- or disease-focused arrays.
This document describes miScript miRNA PCR Arrays, which allow for the simultaneous detection of genome-wide or pathway-focused microRNA (miRNA) expression. It provides an overview of miRNA biology and research, details the miScript miRNA PCR Array system workflow from isolation to data analysis, and discusses applications in cancer research, development, differentiation, and genome-wide discovery. The system offers validated miRNA assays, controls, and optimized reagents to enable reproducible and reliable miRNA expression profiling from RNA samples.
Two-Tailed PCR - New Ultrasensitive and Ultraspecific Technique for the Quant...Kate Barlow
This document discusses methods for quantifying and analyzing microRNAs (miRNAs) using quantitative PCR (qPCR). It presents a new two-tailed RT-qPCR method that provides high sensitivity and specificity for detecting miRNAs, including discrimination of miRNA isoforms. The method allows unlimited multiplexing in the reverse transcription step followed by singleplex qPCR. The document benchmarks the two-tailed RT-qPCR method on biological samples, showing it can sensitively detect less than 10 molecules and maintain specificity across the entire miRNA sequence. It also demonstrates two-tube multiplexing of the method to profile expression levels of several miRNAs in different tissues.
This document describes QIAGEN's RT2 Profiler Plus and RT2 Predictor PCR arrays for assessing pathway activity and cellular toxicity through gene expression analysis. The arrays use curated biomarker gene panels and a mathematical model to generate a pathway activity score from gene expression data. They were developed using extensive validation and have been applied to study pathway regulation during stem cell differentiation, drug effects on pathways, and the role of pathways in cancer stem cells. The Profiler Plus array allows profiling gene expression and calculating a pathway activity score, while the Predictor array calculates the score alone in a higher-throughput format. Both provide a validated method for measuring biological processes using gene expression changes.
This document discusses RNA interference and provides information about QIAGEN's SureSilencing shRNA plasmids for gene knockdown experiments. It begins with an introduction to RNAi mechanisms and challenges. It then describes QIAGEN's SureSilencing shRNA plasmid solution, which features guaranteed high knockdown efficiency, multiple designs to control off-target effects, and experimental validation. The document reviews the plasmid features, design algorithm, applications and provides a workflow for gene knockdown experiments using the plasmids. It emphasizes the importance of including appropriate controls and validation steps to ensure successful RNAi experiments.
This document discusses Wnt signaling and provides an overview of research tools that can be used to study the pathway. It describes the discovery of Wnt proteins and their roles in canonical and noncanonical signaling. The document also reviews the functions of Wnt signaling in development, tissue homeostasis, and various pathological conditions. It proposes using PCR arrays, siRNA, methylation arrays, and reporter assays to develop a Wnt gene signature and measure pathway activity through changes in gene expression and protein levels.
Similar to Reporter assay and q pcr application 2012 (20)
Styles of Scientific Reasoning, Scientific Practices and Argument in Science ...Elsa von Licy
The document discusses various topics related to scientific reasoning, practices, and argumentation including different styles of scientific thinking, features of scientific knowledge, and teaching and learning science. It provides examples of "crazy ideas" in science that are now accepted, examines the role of argument in science, and outlines the scientific practices and central questions of science. It also discusses developing models, planning investigations, analyzing data, and constructing explanations as key scientific practices.
Anti-philosophy rejects traditional philosophy and logic, instead embracing creativity, spirituality, and personality. It considers philosophy to be dead, kept alive artificially by analytic philosophers. The document criticizes how philosophy is currently taught and argues it has become unproductive, replacing original aims with nonsense. Anti-philosophy's goal is not to destroy philosophy but to transform its current state and avoid fundamentalism in philosophy and science.
There is no_such_thing_as_a_social_science_introElsa von Licy
This document provides an introduction and overview of the arguments made in the book "There is No Such Thing as Social Science". It begins by stating the provocative title and questioning whether the authors will take it back or qualify their position.
It then outlines three ways the term "social science" could be used - referring to a scientific spirit of inquiry, a shared scientific method, or reducibility to natural sciences. The authors argue against the latter two, methodological and substantive reductionism.
The introduction discusses how opponents may accuse the authors of being a priori or anti-reductionist, but argues that those defending social science are actually being dogmatic by insisting it must follow a scientific model. It frames the debate as being
1. Webinar
High-Performance Cell-Based
Assay and qPCR Technologies
for Pathway-Focused Research
Louis Lichten, PhD
Application Scientist
5.10.12
For Internal Use Only
-1-
Sample & Assay Technologies
2. Presentation Overview
o QIAGEN’s SABiosciences portfolio
o What is a PCR Array and how do I use it?
o Cignal & Cignal Lenti Pathway Reporters
o Summary
For Internal Use Only
-2-
Sample & Assay Technologies
3. Systems Biology at QIAGEN
Research
DNA
RNA
Gene Expression
Protein
Gene Function
Protein Function
For Internal Use Only
SABiosciences™ Products
Somatic Mutation Arrays
EpiTect ChIP-qPCR Assays
Methyl-Profiler qPCR Arrays
Genomics Service Core
Discovery
Screening
Confirmation
Genomics &
Regulation
Technologies
Mutation Analysis
ChIP
Methylation
SNP/CNV
Genomics Service Core
RT2 PCR Arrays
miScript miRNA Arrays & Assays
RT2 qPCR Assays
Detection
Knockdown
Reporter System
Phenotypes
Cignal Reporter System
ELISArray Kits
siRNA Arrays / shRNA Plasmids
Phosphoprotein Quantitation Kits
-3-
Sample & Assay Technologies
4. Presentation Overview
o QIAGEN’s SABiosciences portfolio
o What is a PCR Array and how do I use it?
o Cignal & Cignal Lenti Pathway Reporters
o Summary
For Internal Use Only
-4-
Sample & Assay Technologies
5. Anatomy of a PCR Array
84 Pathway-Specific
Genes of Interest
5 Housekeeping Genes
Genomic DNA
Contamination Control
Reverse Transcription
Controls (RTC) n=3
Positive PCR Controls
(PPC) n=3
96 well version (1 sample/PCR Array)
(384 well version available (4 samples/PCR Array)
For Internal Use Only
-5-
Sample & Assay Technologies
6. RT2 Profiler PCR Arrays
cDNA Synthesis
45 minutes
.
Load Plates (Preferably with 8Channel Pipettors)
2 minutes
Automated Solution = QIAgility
.
Run 40 cycle qPCR Program
2 to 2.5 hours
Compatible with all major
Real Time PCR Instruments
.
Upload and Analyze Data
15 minutes
.
For Internal Use Only
-6-
Sample & Assay Technologies
7. PCR Arrays for All Biomedical Researchers
Cancer and Apoptosis
Cytokines & Inflammation
Development & Stem Cells
Apoptosis
Inflammatory Cytokines
Stem Cells
Cell Cycle
Th17 for Inflammation (NEW!)
Wnt Signaling
Human miRNA Array (NEW!)
Common Cytokines
Notch Signaling
Breast Cancer & Estrogen Receptor
Chemokines
TGFβ / BMP Signaling
Tumor Metastasis
NF-κB Signaling Pathway
Endothelial Cell Biology
Cancer PathwayFinder
Th1-Th2-Th3
Osteogenesis
Angiogenesis
TNF Ligands
Growth Factors
Cancer Drug Resistance
Toll-like Receptors
ECM & Adhesion
Signal Transduction
Toxicology & Drug Metabolism
Neuroscience
Signal Transduction PathwayFinder
Drug Metabolism
Neuroscience Ion Channels
NFkB Signaling
Drug Phase I Enzymes
Neurotransmitter Receptors
Jak / Stat Signaling
Drug Transporters
Neurotrophins & Receptors
DNA Damage Signaling
Oxidative Stress
Neurogenesis and Neural Stem Cell
Insulin Signaling
Stress & Toxicity
MAP Kinase Signaling
Other Diseases
Custom PCR Arrays
cAMP / Calcium Signaling
Atherosclerosis
96-Well Custom Arrays
p53 Signaling
Diabetes
384-Well Custom Arrays
Complete PCR Array List
For Internal Use Only
-7-
Sample & Assay Technologies
8. Accessing PCR Array Content
For Internal Use Only
-8-
Sample & Assay Technologies
9. PCR Array: Functional Gene Groupings
For Internal Use Only
-9-
Sample & Assay Technologies
11. miScript miRNA PCR Arrays
Complete miRNA genome (miRNome)
miScript miRNA Pathway Arrays
Human miScript miRNA PCR Array
Mouse miScript miRNA PCR Array
Rat miScript miRNA PCR Array
Dog miScript miRNA PCR Array
Species
Number of
assays
Human, Mouse, Rat:
Brain Cancer
Cancer
Cell Differentiation & Development
Immunopathology
Inflammation
miFinder
Neurological Development & Disease
Serum & Plasma
Total Number of Plates
(miRBase V16)
96 well
format
384 well
format
Human
1068
12
3
Mouse
947
12
3
Rat
653
8
2
Dog
277
4
1
For Internal Use Only
- 11 -
Sample & Assay Technologies
12. Custom PCR Arrays – VERY POPULAR!
Analyze the Genes Most Important
To Your Research
• Same reliable and convenient
PCR Array product format
• 2 to 3 week turn around time
• Upload and Analyze Data, just like
our cataloged arrays
For Internal Use Only
- 12 -
Sample & Assay Technologies
13. PCR Array Species Expansion
Species
Cataloged
Array
RNA QC
Array
HKG Array
Custom
Array
Individual
Primer Assays
Human
Y
Y
Y
Y
Y
Mouse
Y
Y
Y
Y
Y
Rat
Y
Y
Y
Y
Y
Rhesus macaque
No
Y
Y
Y
Y
Drosophila
No
Q2 2012
Q2 2012
Y
Y
Dog
No
Y
Y
Y
H2 2012
Pig
No
Y
Q2 2012
Y
H2 2012
Chicken
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Cow
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Zebrafish
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Horse
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Arabidopsis
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Chinese Hamster
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
For Internal Use Only
- 13 -
Sample & Assay Technologies
14. Wet-Bench Validation of ALL qPCR Assays
• Sensitivity
Constant C(t) value for same amount of template
• Amplification Efficiency
DART-PCR analysis
• Specificity
• Single, symmetric dissociation curves
• Single band of appropriate size on agarose gel
• Dynamic Range
Linear over 8 logs of template
• NTC
No primer dimer formation
For Internal Use Only
- 14 -
Sample & Assay Technologies
15. Exceptional Specificity
• Assays on Human TGFβ &
BMP Signaling Pathway
PCR Array used to analyze
BMP genes in Universal
Reference RNA.
• Single peak dissociation
curves
• Single gel bands of
predicted size
• High specificity for genes
difficult to design specific
primers for.
CONCLUSION: Each well on PCR Arrays detects a single gene-specific product.
For Internal Use Only
- 15 -
Sample & Assay Technologies
16. Excellent Reproducibility
Reproducibility Among Different Users
Reproducibility Among Different Instruments
Human Drug Metabolism PCR Array in Universal Reference RNA
CONCLUSION: The PCR Arrays are SO reproducible that the same raw threshold cycle
data can be obtained for the same samples even from different end users at different
times or using different instruments.
For Internal Use Only
- 16 -
Sample & Assay Technologies
19. Summary: PCR Arrays
Complete System for mRNA or miRNA Studies
- Four-component system: sample prep, arrays, master mix, first strand
kit, and free data analysis software
- Four-hour protocol from RNA to presentation-quality results
Breadth of Pathway Content
- More than 100 pathways: human, mouse, rat, monkey, dog
- FULLY CUSTOMIZABLE by gene, set, or pathway
VERY RELIABLE Real-Time PCR Performance
- Wet-bench validation of EVERY primer assay pre-sale
- Melt curve analysis to confirm single amplicon specificity
Hundreds of Peer-Reviewed Articles Using PCR Arrays
http://www.sabiosciences.com/support_publication.php
For Internal Use Only
- 19 -
Sample & Assay Technologies
20. Presentation Overview
o QIAGEN’s SABiosciences portfolio
o What is a PCR Array and how do I use it?
o Cignal & Cignal Lenti Pathway Reporters
o Summary
For Internal Use Only
- 20 -
Sample & Assay Technologies
21. Cignal Reporter Assays (45 Pathways)
Pathway
Amino Acid Deprivation
Androgen
Antioxidant Response
ATF6
C/EBP
cAMP/PKA
Cell Cycle
DNA Damage
EGR1
ER Stress
Estrogen
GATA
Glucocorticoid
Heat Shock Response
Heavy Metal Stress
Hedgehog
HNF4
Hypoxia
Interferon Regulation
Type I Interferon
Interferon Gamma
KLF4
Liver X
For Internal Use Only
Pathway
MAPK/ERK
MAPK/JNK
MEF2
c-myc
Nanog
NFkB
Notch
Oct4
Pax6
PI3K/AKT
PKC/Ca++
PPAR
Progesterone
Retinoic Acid
Retinoid X
Sox2
SP1
STAT3
TGF-beta
VDRE
Wnt
Xenobiotic
Transcription Factor
ATF4/ATF3/ATF2
Androgen Receptor
Nrf2 & Nrf1
ATF6
C/EBP
CREB
E2F/DP1
p53
EGR1
CBF/NF-Y/YY1
ER
GATA
GR
HSF
MTF1
Gli
HNF4
HIF-1
IRF-1
STAT1/STAT2
STAT1/STAT1
KLF4
LXR
- 21 -
Transcription Factor
Elk-1/SRF
AP-1
MEF2
Myc/Max
Nanog
NFkB
RBP-Jk
Oct4
Pax6
FOXO
NFAT
PPAR
PR
RAR
RXR
Sox2
SP1
STAT3
SMAD2/3/4
Vitamin D Receptor
TCF/LEF
AhR
Sample & Assay Technologies
22. Cignal Reporter Assays: Experimental Design
For Internal Use Only
- 22 -
Sample & Assay Technologies
28. Complimentary Arrays: Signal Transduction
•Signal Transduction Pathway Finder
•NFkB Signaling Pathway
•NFkB Signaling Targets
•TGFb Signaling Pathway
•TGFb Signaling Targets
•WNT Signaling Pathway
•WNT Signaling Targets
•Notch Signaling Pathway
•Notch Signaling Targets
For Internal Use Only
- 28 -
Sample & Assay Technologies
29. Cignal Reporters: Benefits & Challenges
Breadth of Pathways and Research Applications
- 45 Pathway-Focused Reporter Assays
- 4 Application-Specific Cignal Finder 10-Pathway Arrays
Convenience
- Ready-to-use, validated, preformatted transient assays
Dual Modalities
- Dual-luciferase quantitative endpoint assays
- GFP dynamic live cell assays with single cell resolution
Biggest Unmet Need for Cignal Researchers
How do I use the Cignal Reporters in cells that
are difficult or impossible to transfect?
For Internal Use Only
- 29 -
Sample & Assay Technologies
30. Cignal Pathway Reporter System Products
Primary cells, stem cells,
and difficult to transfect cell lines
Easy to
transfect cell lines
Endpoint
Assays
Cignal Dual-Luciferase
Reporter Assays
Single Pathway
Assays
For Internal Use Only
10-Pathway
Arrays
Dynamic
Live Cell Assays
Dynamic
Live Cell Assays
Endpoint
Assays
Cignal GFP
Reporter Assays
Cignal Lenti
Luciferase Reporters
Single Pathway
Assays
Single Pathway
Assays
- 30 -
10-Pathway
Arrays
Cignal Lenti
GFP Reporters
Single Pathway
Assays
Sample & Assay Technologies
31. Cignal Lenti Reporter Assays (35 Pathways)
Pathway
Amino Acid Deprivation
Androgen
Antioxidant Response
ATF6
C/EBP
cAMP/PKA
Cell Cycle
DNA Damage
EGR1
ER Stress
Estrogen
GATA
Glucocorticoid
Heat Shock Response
Heavy Metal Stress
Hedgehog
HNF4
Hypoxia
Interferon Regulation
Type I Interferon
Interferon Gamma
KLF4
Liver X
For Internal Use Only
Pathway
MAPK/ERK
MAPK/JNK
MEF2
c-myc
Nanog
NFkB
Notch
Oct4
Pax6
PI3K/AKT
PKC/Ca++
PPAR
Progesterone
Retinoic Acid
Retinoid X
Sox2
SP1
STAT3
TGFβ
VDRE
Wnt
Xenobiotic
Transcription Factor
ATF4/ATF3/ATF2
Androgen Receptor
Nrf2 & Nrf1
ATF6
C/EBP
CREB
E2F/DP1
p53
EGR1
CBF/NF-Y/YY1
ER
GATA
GR
HSF
MTF1
Gli
HNF4
HIF-1
IRF-1
STAT1/STAT2
STAT1/STAT1
KLF4
LXR
- 31 -
Transcription Factor
Elk-1/SRF
AP-1
MEF2
Myc/Max
Nanog
NFkB
RBP-Jk
Oct4
Pax6
FOXO
NFAT
PPAR
PR
RAR
RXR
Sox2
SP1
STAT3
SMAD2/3/4
Vitamin D Receptor
TCF/LEF
AhR
Sample & Assay Technologies
32. Cignal Lenti Reporters: Benefits
Transduce any mammalian cell
– Primary cells
– Stem cells
– Difficult-to-transfect cell lines
Transduction-ready
– No lentiviral generation
– No titering assays
Versatile System
– Transient experiments
– Generate pathway sensor cell
lines
For Internal Use Only
- 32 -
Sample & Assay Technologies
34. NFkB Pathway Sensor Cell Line
Lenti Reporters Enable Rapid Pathway Sensor Cell Line Generation
For Internal Use Only
- 34 -
Sample & Assay Technologies
35. Summary: Cignal Lenti Reporters
.
Breadth of Pathways and Arrays
• 35 Pathway-Focused Reporters
• 2 application-focused Cignal Finder Lenti 10-Pathway Arrays
.
Performance
Exceptional sensitivity, specificity, signal-to-noise ratio, and
reproducibility, using either luciferase or GFP reporter formats
.
High Efficiency Lentiviral Delivery System
• Study cell signaling in primary cells, stem cells, and difficult to
transfect cell lines
• Rapidly generate pathway sensor cell lines
.
Convenience
• Ready-to-use, validated reporters
• Don’t have to produce or amplify lentivirus in your laboratory
For Internal Use Only
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Sample & Assay Technologies
36. Take Home Message
Tell a better Biological Story from your experiments
• Publish faster and in higher impact journals
• Work SMARTER, NOT Harder
• Improve Success Rates of Your Grant Applications
• Expedite Drug Pipeline
For Internal Use Only
- 36 -
Sample & Assay Technologies