Primer design and transcript quantification of a highly multiplexed RT‐PCR for a nonmodel avian species

2011 ◽  
Vol 12 (1) ◽  
pp. 116-122 ◽  
Author(s):  
SUSAN L. BALENGER ◽  
CHRISTOPHER J. W. McCLURE ◽  
GEOFFREY E. HILL
BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Paulo Rapazote-Flores ◽  
Micha Bayer ◽  
Linda Milne ◽  
Claus-Dieter Mayer ◽  
John Fuller ◽  
...  

Abstract Background The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants. Results A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts – BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427–433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20–28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5′ and 3′ UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage. Conclusion A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.


2015 ◽  
Vol 23 (2) ◽  
Author(s):  
Adrian Man ◽  
Claudia Bănescu ◽  
Minodora Dobreanu ◽  
Cornel Fraefel

AbstractSuccessful experiments in molecular biology require good knowledge about various methods and protocols. In molecular biology, nucleic acid manipulation is the essence, starting with the quality of extraction and ending with several analysis assays (PCR, RT-PCR, qPCR, PCR arrays, molecular cloning, etc). Though many of these are so called “standardized”, in practice there are many variables that can influence the outcome of the experiment. Due to the importance of optimal primer design in PCR assays, we will focus on primer designing and checking software, but we also present other useful free tools that can help researchers in the molecular biology field


Author(s):  
Kelvin Li ◽  
Anushka Brownley
Keyword(s):  

2017 ◽  
Author(s):  
Pauline Marquardt ◽  
Britta Werthmann ◽  
Viktoria Rätzel ◽  
Markus Haas ◽  
Wolfgang Marwan

AbstractQuantitative analysis of differential gene expression is of central importance in molecular life sciences. The Gene eXpression Profiling technology (GeXP) relies on multiplex RT-PCR and subsequent capillary electrophoretic separation of the amplification products and allows to quantify the transcripts of up to approximately 35 genes with a single reaction and one dye. Here, we provide a kinetic model of primer binding and PCR product formation as the rational basis for taking and evaluating calibration curves. With the help of a purposeful designed data processing workflow supported by easy-to-use Perl scripts for calibration, data evaluation, and quality control, the calibration procedure and the model predictions were confirmed and the robustness and linearity of transcript quantification demonstrated for differentiating Physarum polycephalum plasmodial cells. We conclude that GeXP analysis is a robust, sensitive, and useful method when the transcripts of tens to few hundred genes are to be precisely quantified in a high number of samples.


1997 ◽  
Vol 25 (9) ◽  
pp. 1830-1835 ◽  
Author(s):  
R. Fislage ◽  
M. Berceanu ◽  
Y. Humboldt ◽  
M. Wendt ◽  
H. Oberender

2019 ◽  
Author(s):  
Paulo Rapazote-Flores ◽  
Micha Bayer ◽  
Linda Milne ◽  
Claus-Dieter Mayer ◽  
John Fuller ◽  
...  

AbstractBackgroundTime consuming computational assembly and quantification of gene expression and splicing analysis from RNA-seq data vary considerably. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.ResultsA high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts – BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al., 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al., 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5’ and 3’ UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2,791 differentially alternatively spliced genes and 2,768 transcripts with differential transcript usage.ConclusionA high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3015-3015
Author(s):  
Claudia Scholl ◽  
Karina Eiwen ◽  
Stefan Frohling ◽  
Richard F. Schlenk ◽  
Hartmut Dohner ◽  
...  

Abstract Detection of minimal residual disease (MRD) in acute myeloid leukemia (AML) with specific gene fusions is an important tool for the assessment of response to treatment and the individual risk of relapse. We evaluated the predictive value of MLL/AF9 fusion-transcript quantification using real-time RT-PCR for disease relapse and verified the results with nested RT-PCR. A t(9;11) was identified in 27 younger AML patients (16–60 years) entered into the multicenter trials AML HD93 and AML HD98-A of the AML Study Group Ulm. One hundred seventy-eight samples (bone marrow [BM], n=84; peripheral blood [PB], n=79; leukapheresis product [LP], n=15) from 22 patients were available for real-time RT-PCR analysis. In 6 of these 22 patients, only samples from diagnosis were obtained, the remaining 16 patients were analyzed during and after therapy. The sensitivity of the real-time RT-PCR was 10−3 and of the nested RT-PCR 10−4 to 10−5. The MLL/AF9 copy number at diagnosis was not predictive of subsequent clinical outcome. Eight of the 16 evaluable patients became real-time RT-PCR-negative after double induction therapy. Six of these 8 patients are in continuous complete remission (CR), 1 died in CR from graft-versus-host disease, and 1 relapsed 11 months after diagnosis. Eight of 16 patients had detectable fusion-transcript levels after achieving complete hematologic remission. Six of these 8 patients relapsed after a median of 8.6 months (range, 3.6 to 13.5) from diagnosis, one patient died in CR 3 weeks after autologous BM transplantation, and one patient underwent allogeneic BM transplantation and is in continuous CR 16 months after diagnosis. Of 3 patients, who relapsed, we were able to analyze bone marrow 1 months before hematologic relapse occurred. Two of these 3 patients were real-time RT-PCR-negative after therapy and became positive 1 month before relapse, 1 patient was still real-time RT-PCR-positive after therapy and had increased MLL/AF9 copy numbers 1 month before relapse occurred. Five Patients, who were in continuous CR, were real-time RT-PCR-negative in all analyzed samples during follow up (median, 56 months; range, 13.8 to 68.9 months). One hundred seventy-two patient samples were examined by nested RT-PCR. Real-time RT-PCR-negative samples were also negative with nested RT-PCR, therefore nested RT-PCR did not enhance sensitivity of real-time PCR. We conclude that real-time RT-PCR is convenient for the detection of MRD in t(9;11)-positive AML and real-time RT-PCR positivity in at least one sample during therapy correlates with a high risk of relapse.


2016 ◽  
Vol 18 (1) ◽  
pp. 84-91 ◽  
Author(s):  
Lida Chen ◽  
Wenli Li ◽  
Kuo Zhang ◽  
Rui Zhang ◽  
Tian Lu ◽  
...  

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Fangzhou Zhao ◽  
Nathan A. Maren ◽  
Pawel Z. Kosentka ◽  
Ying-Yu Liao ◽  
Hongyan Lu ◽  
...  

AbstractComputational tool-assisted primer design for real-time reverse transcription (RT) PCR (qPCR) analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome. It can lead to false confidence in the quality of the designed primers, which sometimes results in skipping the optimization steps for qPCR. However, the optimization of qPCR parameters plays an essential role in the efficiency, specificity, and sensitivity of each gene’s primers. Here, we proposed an optimized approach to sequentially optimizing primer sequences, annealing temperatures, primer concentrations, and cDNA concentration range for each reference (and target) gene. Our approach started with a sequence-specific primer design that should be based on the single-nucleotide polymorphisms (SNPs) present in all the homologous sequences for each of the reference (and target) genes under study. By combining the efficiency calibrated and standard curve methods with the 2−ΔΔCt method, the standard cDNA concentration curve with a logarithmic scale was obtained for each primer pair for each gene. As a result, an R2 ≥ 0.9999 and the efficiency (E) = 100 ± 5% should be achieved for the best primer pair of each gene, which serve as the prerequisite for using the 2−ΔΔCt method for data analysis. We applied our newly developed approach to identify the best reference genes in different tissues and at various inflorescence developmental stages of Tripidium ravennae, an ornamental and biomass grass, and validated their utility under varying abiotic stress conditions. We also applied this approach to test the expression stability of six reference genes in soybean under biotic stress treatment with Xanthomonas axonopodis pv. glycines (Xag). Thus, these case studies demonstrated the effectiveness of our optimized protocol for qPCR analysis.


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