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QPCR: Application for real-time PCR data management and analysis

Stephan Pabinger, Gerhard G Thallinger, René Snajder, Heiko Eichhorn, Robert Rader, Zlatko Trajanoski
2009 BMC Bioinformatics  
Since its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression.  ...  Results: QPCR is a versatile web-based Java application that allows to store, manage, and analyze data from relative quantification qPCR experiments.  ...  We thank Anne Krogsdam and Andreas Prokesch for valuable discussions and Roman Fiedler for implementing the initial file parser.  ... 
doi:10.1186/1471-2105-10-268 pmid:19712446 pmcid:PMC2741456 fatcat:fonten77vrcz7myjv4c4byffpe

The ongoing evolution of qPCR

Michael W. Pfaffl
2010 Methods  
the MIQE (minimum information for publication of quan-titative real-time PCR experiments) guidelines?  ...  Accurate and straightforward mathematical and statistical analysis of qPCR data and the related data management of these growing data sets have become major hurdles to effective implementation.  ... 
doi:10.1016/j.ymeth.2010.02.005 pmid:20215019 fatcat:ocwzjqgnifexrfcjfapcj4pc24

AScall – Automatic Allele-Specific qPCR Analysis

Konstantin Blagodatskikh, Dmitrii Romaniuk, Dmitry Malko
2020 Frontiers in Bioengineering and Biotechnology  
To determine the genetic mismatches between a donor and a recipient, we have implemented a real-time PCR method in conjunction with allele-specific primers (AS-qPCR).  ...  Earlier, we have confirmed and published the AS-qPCR method, but standard software for qPCR analysis does not suit AS-qPCR data.  ...  We picked AS-PCR variation conducted with hydrolysis probes in real-time (designated from here on as AS-qPCR) (Stadhouders et al., 2010) .  ... 
doi:10.3389/fbioe.2020.00353 pmid:32391349 pmcid:PMC7188954 fatcat:wv2izmliera5hhqnghy6pvnipq

Auto-qPCR: A Python based web app for automated and reproducible analysis of qPCR data [article]

Gilles Maussion, Rhalena A. Thomas, Iveta Demirova, Gracia Gu, Eddie Cai, Carol X.-Q. Chen, Narges Abdian, Theodore J.P. Strauss, Sabah Kelai, Angela Nauleau Javaudin, Lenore K Beitel, Nicolas Ramoz (+2 others)
2021 bioRxiv   pre-print
Quantitative real time PCR (qPCR) techniques, in both clinical and basic research labs, have evolved to become both routine and standardized.  ...  Auto-qPCR also includes options for statistical analysis of the data.  ...  Real-time PRC (RT-PCR) was performed on a QuantStudio 3 machine (Thermo Fisher Scientific).  ... 
doi:10.1101/2021.01.14.426748 fatcat:2ohahyrshfei7cfznuxyps5oty

qPCR-DAMS: a database tool to analyze, manage, and store both relative and absolute quantitative real-time PCR data

Nili Jin, Keyu He, Lin Liu
2006 Physiological Genomics  
In summary, qPCR-DAMS is a handy tool for real-time PCR users. quantitative PCR data analysis and management system QUANTITATIVE REAL-TIME PCR (qPCR) is becoming increasingly important in biomedical research  ...  The quantitative PCR data analysis and management system (qPCR-DAMS) software provides a single software package to process, manage, and store both relative and absolute quantitative real-time PCR data  ...  ACKNOWLEDGMENTS We are grateful to Zhongming Chen, Tingting Weng, and Manoj Bhaskaran, who gave many constructive suggestions. We also thank Tisha Posey for editorial assistance.  ... 
doi:10.1152/physiolgenomics.00233.2005 pmid:16507784 fatcat:jxxgkoyubjcnrgfy6ueqacag24

Development and Validation of qPCR and RT-qPCR: Regulatory Points to Consider When Conducting Biodistribution and Vector Shedding Studies of Gene and Cell Therapy Products

Haiyan Ma, Kristin N. Bell, Rossi N. Loker
2020 Molecular Therapy: Methods & Clinical Development  
With regard to this need, we offer critical points to consider when developing, validating, running sample analysis, and reporting qPCR/qRT-PCR assays.  ...  There is an urgent need for an ongoing discussion among bioanalytical scientists in this field to generate a "best practice" consensus around preclinical and clinical qPCR/qRT-PCR assay design.  ...  ACKNOWLEDGMENTS We are grateful for Dr. Joshua T. Bartoe for his kind review of the manuscript.  ... 
doi:10.1016/j.omtm.2020.11.007 pmid:33473355 pmcid:PMC7786041 fatcat:7rywvnwsdfbcfo5tp3n4er7zr4

A qPCR method to quantify bioavailable phosphorus using indigenous aquatic species

Yanan Yang, Jianghua Yang, Xiaowei Zhang
2018 Environmental Sciences Europe  
The specificity and efficiency of the primer sets were evaluated by gel electrophoresis and real-time PCR.  ...  Results: Here, a quantitative real-time PCR (qPCR)-based bioassay was developed to quantify BAP using the indigenous cyanobacterium species Anabaena sp. of Lake Tai, a large and shallow eutrophic lake  ...  Acknowledgements Not applicable.  ... 
doi:10.1186/s12302-018-0163-z pmid:30221104 pmcid:PMC6132795 fatcat:zxiygjr6tjdtxmyrii7qcjz2le

SASqPCR: Robust and Rapid Analysis of RT-qPCR Data in SAS

Daijun Ling, Martin Beer
2012 PLoS ONE  
Reverse transcription quantitative real-time PCR (RT-qPCR) is a key method for measurement of relative gene expression.  ...  Analysis of RT-qPCR data requires many iterative computations for data normalization and analytical optimization.  ...  Analyzed the data: DL. Contributed reagents/materials/analysis tools: DL. Wrote the paper: DL.  ... 
doi:10.1371/journal.pone.0029788 pmid:22238653 pmcid:PMC3253109 fatcat:ufo75kq7ibewzn6dg2h3tlvi2i

Single-cell qPCR Assay with Massively Parallel Microfluidic System

Marta Prieto-Vila, Takahiro Ochiya, Yusuke Yamamoto
2020 Bio-protocol  
The main steps for single-cell qPCR, as illustrated in this protocol, are composed by single-cell isolation, cell lysate, cDNA reverse-transcription synthesis, amplification for cDNA library generation  ...  It is extremely variable and changes according to external, physical and biochemical conditions.  ...  Acknowledgments The present work was supported in part by a Grant-in-Aid for Scientific Research (C) JSPS  ... 
doi:10.21769/bioprotoc.3563 pmid:33659534 pmcid:PMC7842821 fatcat:kabkboc3fjdgxedi3cz6l4vxx4

Sample-ready multiplex qPCR assay for detection of malaria

Edwin Kamau, Saba Alemayehu, Karla C Feghali, Dennis W Juma, George M Blackstone, William R Marion, Peter Obare, Bernhards Ogutu, Christian F Ockenhouse
2014 Malaria Journal  
However, due to their limitations, the need to utilize more sensitive methods such as real-time PCR (qPCR) is evident as more studies are now utilizing molecular methods in detection of malaria.  ...  Availability of MMSR assay allows flexibility and provides an option in choosing assay for malaria diagnostics depending on the application, needs and budget.  ...  There is no objection to its presentation and/or publication.  ... 
doi:10.1186/1475-2875-13-158 pmid:24767409 pmcid:PMC4026594 fatcat:is3sixbcerecdezxupo53b4khu

Addressing fluorogenic real-time qpcr inhibition using the novel custom excel file system 'FocusField2-6GallupqPCRSet-upTool-001' to attain consistently high fidelity qPCR reactions

Jack M. Gallup, Mark R. Ackermann
2006 Biological Procedures Online 88 biology for quantitative analysis of gene expression, and since it is still considered the tool of choice for validating micro-array data, any new ideas, methods or approaches  ...  Gallup and Ackermann -Addressing fluorogenic real-time qPCR inhibition using the novel custom Excel file system 'FocusField2-6GallupqPCRSet-upTool-001' to attain consistently high fidelity qPCR reactions  ...  In two-step real-time qPCR applications, ten other Excel files are activated which all function to correctly handle cDNA preparation and its subsequent use in qPCR as managed by the FF2-6-001 qPCR set-up  ... 
doi:10.1251/bpo122 pmid:17033699 pmcid:PMC1592462 fatcat:zsq23jczhre5rjyhehro5lxyse

LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species

Henning Hanschmann, Stefan Rödiger, Toni Kramer, Katrin Hanschmann, Michael Steidle, Volker Fingerle, Carsten Schmidt, Werner Lehmann, Peter Schierack
2021 Life  
Conclusion: We established a novel multiplex probe real-time PCR system, designated LoopTag, that is simple, robust, and incorporates melting curve analysis for the detection and in the differentiation  ...  multiplex real-time PCRs, melting curve analysis (single nucleotide polymorphism analysis) over a large temperature range, high sensitivity, and easy adaptation of conventional PCRs.  ...  Materials and Methods qPCR Reaction and Melting Curve Analysis Real-time PCRs were performed with a LightCycler® 1.5 and a LightCycler® 2.0 (Roche, Germany) using LightCycler® FastStart DNA Master HybProbe  ... 
doi:10.3390/life11111163 pmid:34833039 pmcid:PMC8624210 fatcat:2a47b6a7ojatvbz4buiwdltdkq

Survivin isoforms and clinicopathological characteristics in colorectal adenocarcinomas using real-time qPCR

Anastasia Pavlidou
2011 World Journal of Gastroenterology  
Real time quantitative polymerase chain reaction (PCR) was performed on cDNAs from 52 tumor specimens from colorectal cancer patients and 10 unrelated normal colorectal tissues.  ...  METHODS: We used the LightCycler Technology (Roche), along with a common forward primer and reverse primers specific for the splice variants and two common hybridization probes labeled with fluorescein  ...  accurate and sensitive real time-qPCR in the Lightcycler platform.  ... 
doi:10.3748/wjg.v17.i12.1614 pmid:21472129 pmcid:PMC3070134 fatcat:clbznrljb5abhede7arjhfnyyi

Handheld Continuous-flow Real-time Fluorescence qPCR System with PVC Microreactor

Bing Shi, Yuanming Li, Di Wu, Wenming Wu
2020 The Analyst  
The polymerase chain reaction (PCR) has unique advantages of sensitivity, specificity and rapidity in pathogen detection, which makes it at the forefront of academia and application in molecular biology  ...  This project was supported by the CAS Pioneer Hundred Talents Program, the National Natural Science Foundation of China (no. 61704169), the Natural Science Foundation of Jilin Province (20180520112JH), and  ...  Based on the above data analysis, it can be con- cluded that the PVC material is superior to PTFE for fluorescence excitation and detection during qPCR.  ... 
doi:10.1039/c9an01894h pmid:32095799 fatcat:dviiiflvdfavdbsxxitsr6g5mm

A survey of tools for the analysis of quantitative PCR (qPCR) data

Stephan Pabinger, Stefan Rödiger, Albert Kriegner, Klemens Vierlinger, Andreas Weinhäusel
2014 Biomolecular Detection and Quantification  
Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research.  ...  Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR.  ...  It is designed to analyze, manage, and store relative as well as absolute quantitative real-time PCR data.  ... 
doi:10.1016/j.bdq.2014.08.002 pmid:27920994 pmcid:PMC5129434 fatcat:ogcslo3tgfewjdlm6tdpcgixia
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