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Casmil IC, Huang C, Blakney AK. A duplex droplet digital PCR assay for absolute quantification and characterization of long self-amplifying RNA. Sci Rep 2023; 13:19050. [PMID: 37923834 PMCID: PMC10624827 DOI: 10.1038/s41598-023-46314-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
Self-amplifying messenger ribonucleic acid (saRNA) provides extended expression of genes of interest by encoding an alphavirus-derived RNA replicase and thus is 2-3 times larger than conventional messenger RNA. However, quality assessment of long RNA transcripts is challenging using standard techniques. Here, we utilized a multiplex droplet digital polymerase chain reaction (ddPCR) assay to assess the quality of saRNA produced from an in vitro transcription reaction and the replication kinetics in human cell lines. Using the one-step reverse transcription ddPCR, we show that an in vitro transcription generates 50-60% full-length saRNA transcripts. However, we note that the two-step reverse transcription ddPCR assay results in a 20% decrease from results obtained using the one-step and confirmed using capillary gel electrophoresis. Additionally, we provided three formulas that differ in the level of stringency and assumptions made to calculate the fraction of intact saRNA. Using ddPCR, we also showed that subgenomic transcripts of saRNA were 19-to-108-fold higher than genomic transcripts at different hours post-transfection of mammalian cells in copies. Therefore, we demonstrate that multiplex ddPCR is well suited for quality assessment of long RNA and replication kinetics of saRNA based on absolute quantification.
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Affiliation(s)
- Irafasha C Casmil
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cynthia Huang
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Anna K Blakney
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Carmona-Molero R, Jimenez-Lopez JC, Caballo C, Gil J, Millán T, Die JV. Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea. PLANTS 2021; 10:plants10112429. [PMID: 34834791 PMCID: PMC8619295 DOI: 10.3390/plants10112429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 11/04/2021] [Indexed: 11/23/2022]
Abstract
Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class with promising potential for plant adaptation improvement. Aldehyde dehydrogenases constitute a superfamily of proteins with important functions as ‘aldehyde scavengers’ by detoxifying aldehydes molecules, and thus play important roles in stress responses. We performed a comprehensive study of the ALDH superfamily in the chickpea genome and identified 27 unique ALDH loci. Most chickpea ALDHs originated from duplication events and the ALDH3 gene family was noticeably expanded. Based on the physical locations of genes and sequence similarities, our results suggest that segmental duplication is a major driving force in the expansion of the ALDH family. Supported by expression data, the findings of this study offer new potential target genes for improving stress tolerance in chickpea that will be useful for breeding programs.
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Affiliation(s)
- Rocío Carmona-Molero
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell and Molecular Biology of Plants, EEZ-CSIC, 18008 Granada, Spain;
- Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth 6009, Australia
| | - Cristina Caballo
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, 14080 Córdoba, Spain;
| | - Juan Gil
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Teresa Millán
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
| | - Jose V. Die
- Department of Genetics ETSIAM, University of Córdoba, 14071 Córdoba, Spain; (R.C.-M.); (J.G.); (T.M.)
- Correspondence:
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Development of a 3':5' digital PCR assay to determine horse mRNA integrity. Anal Biochem 2021; 626:114217. [PMID: 33939972 DOI: 10.1016/j.ab.2021.114217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Accurate tools to measure RNA integrity are essential to obtain reliable gene expression data. The reverse transcription quantitative PCR (RT-qPCR) based 3':5' assay permits a direct determination of messenger RNA (mRNA) integrity. However, the use of standard curves and the possible effect of PCR inhibitors make this method cumbersome and prone to variation, especially in small samples. Here we developed a triplex digital PCR (dPCR) 3':5' assay for assessing RNA integrity in equine samples as rapid and simple alternative to RT-qPCR. This dPCR assay not only provides a straight forward analysis of the mRNA integrity, but also of its quantity.
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Characterization and Analysis of Anthocyanin-Related Genes in Wild-Type Blueberry and the Pink-Fruited Mutant Cultivar ‘Pink Lemonade’: New Insights into Anthocyanin Biosynthesis. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Blueberries are one of the richest sources of antioxidants, such as anthocyanins, among fruits and vegetables. Anthocyanin mutants, like the pink-fruited cultivar ‘Pink Lemonade’, are valuable resources for investigating anthocyanin biosynthesis in blueberries. In this study, we examined expression of flavonoid pathway genes during fruit development in wild-type, blue-fruited blueberries using quantitative real-time PCR. Expression was also compared between wild-type and the pink-fruited ‘Pink Lemonade’. This revealed significantly lower expression in ‘Pink Lemonade’ than in wild-type of nearly all the structural genes examined suggesting that a transcriptional regulator of the pathway was affected. Hence, we compared expression of three known regulatory genes and found that the gene encoding the transcription factor MYB1 was expressed at a significantly lower level in ‘Pink Lemonade’ than in the wild-type. To validate the capacity of this MYB1 to regulate the transcription of anthocyanin genes in blueberries, a transient expression assay was conducted. Results indicated MYB1 overexpression enhanced anthocyanin production. Comparative sequence analysis between wild-type and mutant MYB1 variants found differences in highly conserved features suggesting a mechanistic explanation for the mutant phenotype. Collectively, the results presented here contribute to a better understanding of mechanisms regulating anthocyanin biosynthesis in Vaccinium.
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Rochow H, Franz A, Jung M, Weickmann S, Ralla B, Kilic E, Stephan C, Fendler A, Jung K. Instability of circular RNAs in clinical tissue samples impairs their reliable expression analysis using RT-qPCR: from the myth of their advantage as biomarkers to reality. Am J Cancer Res 2020; 10:9268-9279. [PMID: 32802191 PMCID: PMC7415809 DOI: 10.7150/thno.46341] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Circular RNAs (circRNAs) are a new class of RNAs with medical significance. Compared to that of linear mRNA transcripts, the stability of circRNAs against degradation owing to their circular structure is considered advantageous for their use as biomarkers. As systematic studies on the stability of circRNAs depending on the RNA integrity, determined as RNA integrity number (RIN), in clinical tissue samples are lacking, we have investigated this aspect in the present study under model and clinical conditions. Methods: Total RNA isolated from kidney cancer tissue and cell lines (A-498 and HEK-293) with different RIN after thermal degradation was used in model experiments. Further, RNA isolated from kidney cancer and prostate cancer tissue collected under routine surgical conditions, representing clinical samples with RIN ranging from 2 to 9, were examined. Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) analysis of several circRNAs (circEGLN3, circRHOBTB3, circCSNK1G3, circRNA4, and circRNA9), their corresponding linear counterparts, tissue-specific reference genes, and three microRNAs (as controls) was performed. The quantification cycles were converted into relative quantities and normalized to the expression of specific reference genes for the corresponding tissue. The effect of RIN on the expression of different RNA entities was determined using linear regression analysis, and clinical samples were classified into two groups based on RIN greater or lesser than 6. Results: The results of model experiments and clinical sample analyses showed that all relative circRNA expression gradually decreased with reduction in RIN values. The adverse effect of RIN was partially compensated after normalizing the data and limiting the samples to only those with RIN values > 6. Conclusions: Our results suggested that circRNAs are not stable in clinical tissue samples, but are subjected to degradative processes similar to mRNAs. This has not been investigated extensively in circRNA expression studies, and hence must be considered in future for obtaining reliable circRNA expression data. This can be achieved by applying the principles commonly used in mRNA expression studies.
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Esteva-Socias M, Artiga MJ, Bahamonde O, Belar O, Bermudo R, Castro E, Escámez T, Fraga M, Jauregui-Mosquera L, Novoa I, Peiró-Chova L, Rejón JD, Ruiz-Miró M, Vieiro-Balo P, Villar-Campo V, Zazo S, Rábano A, Villena C. In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network. J Transl Med 2019; 17:370. [PMID: 31718661 PMCID: PMC6852937 DOI: 10.1186/s12967-019-2124-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/01/2019] [Indexed: 01/10/2023] Open
Abstract
The purpose of the present work is to underline the importance of obtaining a standardized procedure to ensure and evaluate both clinical and research usability of human tissue samples. The study, which was carried out by the Biospecimen Science Working Group of the Spanish Biobank Network, is based on a general overview of the current situation about quality assurance in human tissue biospecimens. It was conducted an exhaustive review of the analytical techniques used to evaluate the quality of human tissue samples over the past 30 years, as well as their reference values if they were published, and classified them according to the biomolecules evaluated: (i) DNA, (ii) RNA, and (iii) soluble or/and fixed proteins for immunochemistry. More than 130 publications released between 1989 and 2019 were analysed, most of them reporting results focused on the analysis of tumour and biopsy samples. A quality assessment proposal with an algorithm has been developed for both frozen tissue samples and formalin-fixed paraffin-embedded (FFPE) samples, according to the expected quality of sample based on the available pre-analytical information and the experience of the participants in the Working Group. The high heterogeneity of human tissue samples and the wide number of pre-analytic factors associated to quality of samples makes it very difficult to harmonize the quality criteria. However, the proposed method to assess human tissue sample integrity and antigenicity will not only help to evaluate whether stored human tissue samples fit for the purpose of biomarker development, but will also allow to perform further studies, such as assessing the impact of different pre-analytical factors on very well characterized samples or evaluating the readjustment of tissue sample collection, processing and storing procedures. By ensuring the quality of the samples used on research, the reproducibility of scientific results will be guaranteed.
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Affiliation(s)
- Margalida Esteva-Socias
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
| | | | | | - Oihana Belar
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Raquel Bermudo
- Hospital Clínic-IDIBAPS Biobank, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Erika Castro
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Teresa Escámez
- IMIB Biobank, Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Máximo Fraga
- Depto. de Ciencias Forenses, Anatomía Patolóxica, Xinecología e Obstetricia, e Pediatría, Facultade de Medicina, Universidade de Santiago de Compostela (USC), Santiago, Spain.,Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Isabel Novoa
- Vall d'Hebron University Hospital Biobank, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | | | - Juan-David Rejón
- Biobanco del Sistema Sanitario Público de Andalucía, Granada, Spain
| | - María Ruiz-Miró
- IRBLleida Biobank, Instituto de Investigaciones Biomédica de Lleida-Fundación Dr. Pifarre, Lérida, Spain
| | - Paula Vieiro-Balo
- Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Sandra Zazo
- Department of Pathology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Alberto Rábano
- Banco de Tejidos, Fundación CIEN, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Villena
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain. .,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain.
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Qi X, Ogden EL, Die JV, Ehlenfeldt MK, Polashock JJ, Darwish O, Alkharouf N, Rowland LJ. Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations. BMC PLANT BIOLOGY 2019; 19:460. [PMID: 31711416 PMCID: PMC6844065 DOI: 10.1186/s12870-019-2073-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/14/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Blueberry is of high economic value. Most blueberry varieties selected for the fresh market have an appealing light blue coating or "bloom" on the fruit due to the presence of a visible heavy epicuticular wax layer. This waxy layer also serves as natural defense against fruit desiccation and deterioration. RESULTS In this study, we attempted to identify gene(s) whose expression is related to the protective waxy coating on blueberry fruit utilizing two unique germplasm populations that segregate for the waxy layer. We bulked RNA from waxy and non-waxy blueberry progenies from the two northern-adapted rabbiteye hybrid breeding populations ('Nocturne' x T 300 and 'Nocturne' x US 1212), and generated 316.85 million RNA-seq reads. We de novo assembled this data set integrated with other publicly available RNA-seq data and trimmed the assembly into a 91,861 blueberry unigene collection. All unigenes were functionally annotated, resulting in 79 genes potentially related to wax accumulation. We compared the expression pattern of waxy and non-waxy progenies using edgeR and identified overall 1125 genes in the T 300 population and 2864 genes in the US 1212 population with at least a two-fold expression difference. After validating differential expression of several genes by RT-qPCR experiments, a candidate gene, FatB, which encodes acyl-[acyl-carrier-protein] hydrolase, emerged whose expression was closely linked to the segregation of the waxy coating in our populations. This gene was expressed at more than a five-fold higher level in waxy than non-waxy plants of both populations. We amplified and sequenced the cDNA for this gene from three waxy plants of each population, but were unable to amplify the cDNA from three non-waxy plants that were tested from each population. We aligned the Vaccinium deduced FATB protein sequence to FATB protein sequences from other plant species. Within the PF01643 domain, which gives FATB its catalytic function, 80.08% of the amino acids were identical or had conservative replacements between the blueberry and the Cucumis melo sequence (XP_008467164). We then amplified and sequenced a large portion of the FatB gene itself from waxy and non-waxy individuals of both populations. Alignment of the cDNA and gDNA sequences revealed that the blueberry FatB gene consists of six exons and five introns. Although we did not sequence through two very large introns, a comparison of the exon sequences found no significant sequence differences between the waxy and non-waxy plants. This suggests that another gene, which regulates or somehow affects FatB expression, must be segregating in the populations. CONCLUSIONS This study is helping to achieve a greater understanding of epicuticular wax biosynthesis in blueberry. In addition, the blueberry unigene collection should facilitate functional annotation of the coming chromosomal level blueberry genome.
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Affiliation(s)
- Xinpeng Qi
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
| | - Elizabeth L. Ogden
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
| | - Jose V. Die
- Departmento de Genetica, University of Córdoba Campus Rabanales, Blg. C5, 14071 Córdoba, Spain
| | - Mark K. Ehlenfeldt
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, at Rutgers University P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019 USA
| | - James J. Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, at Rutgers University P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019 USA
| | - Omar Darwish
- Department of Mathematics and Computer Science, Texas Woman’s University, Denton, TX 76204 USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252 USA
| | - L. Jeannine Rowland
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
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8
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Caballo C, Castro P, Gil J, Millan T, Rubio J, Die JV. Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5. PLoS One 2019; 14:e0224212. [PMID: 31644597 PMCID: PMC6808423 DOI: 10.1371/journal.pone.0224212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/08/2019] [Indexed: 01/23/2023] Open
Abstract
Chickpea production may be seriously threatened by Fusarium wilt, a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. ciceris. F. oxysporum race 5 is the most important race in the Mediterranean basin. Recently, the region responsible for resistance race 5 has been delimited within a region on chromosome 2 that spans 820 kb. To gain a better understanding of this genomic region, we used a transcriptomic approach based on quantitative real-time PCR to analyze the expression profiles of 22 selected candidate genes. We used a pair of near-isogenic lines (NILs) differing in their sensitivity to Fusarium race 5 (resistant vs susceptible) to monitor the transcriptional changes over a time-course experiment (24, 48, and 72 hours post inoculation, hpi). Qualitative differences occurred during the timing of regulation. A cluster of 12 genes were induced by the resistant NIL at 24 hpi, whereas a second cluster contained 9 genes induced by the susceptible NIL at 48 hpi. Their possible functions in the molecular defence of chickpea is discussed. Our study provides new insight into the molecular defence against Fusarium race 5 and demonstrates that development of NILs is a rich resource to facilitate the detection of candidate genes. The new genes regulated here may be useful against other Fusarium races.
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Affiliation(s)
- Cristina Caballo
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, Córdoba, Spain
| | - Patricia Castro
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Juan Gil
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Teresa Millan
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Josefa Rubio
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, Córdoba, Spain
| | - Jose V. Die
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
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Application of the CRISPRi system to repress sepF expression in Mycobacterium smegmatis. INFECTION GENETICS AND EVOLUTION 2019; 72:183-190. [DOI: 10.1016/j.meegid.2018.06.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 11/22/2022]
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10
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Cholet F, Ijaz UZ, Smith CJ. Differential ratio amplicons (R amp ) for the evaluation of RNA integrity extracted from complex environmental samples. Environ Microbiol 2019; 21:827-844. [PMID: 30585386 PMCID: PMC6392129 DOI: 10.1111/1462-2920.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022]
Abstract
Reliability and reproducibility of transcriptomics‐based studies are dependent on RNA integrity. In microbial ecology, microfluidics‐based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here, we present an integrity index, the Ratio Amplicon, Ramp, adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly‐degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT‐Q‐PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this, both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study.
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Affiliation(s)
- Fabien Cholet
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Cindy J Smith
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
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11
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Die JV, Gil J, Millan T. Genome-wide identification of the auxin response factor gene family in Cicer arietinum. BMC Genomics 2018; 19:301. [PMID: 29703137 PMCID: PMC5921756 DOI: 10.1186/s12864-018-4695-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/18/2018] [Indexed: 02/06/2023] Open
Abstract
Background Auxin Response Factors act as critical components of the auxin-signaling pathway by regulating the transcription of auxin-responsive genes. The release of the chickpea reference genome provides an opportunity to identify and characterize the ARF gene family in this important legume by a data mining coupled by comparative genomics approaches. Results We performed a comprehensive characterization and analysis of 24 ARF genes in the chickpea reference genome. Comparative phylogenetic analysis of the ARF from chickpea, Medicago and Arabidopsis suggests that recent duplications have played a very limited role in the expansion of the ARF chickpea family. Gene structure analysis based on exon-intron organization provides additional evidence to support the evolutionary relationship among the ARF members. Conserved motif analysis shows that most of the proteins fit into the canonical ARF structure model, but 9 proteins lack or have a truncated dimerization domain. The mechanisms underlying the diversification of the ARF gene family are based on duplications, variations in domain organization and alternative splicing. Concerning duplications, segmental, but not tandem duplications, have contributed to the expansion of the gene family. Moreover, the duplicated pair genes have evolved mainly under the influence of purifying selection pressure with restricted functional divergence. Expression profiles responding to various environmental stimuli show a close relationship between tissue and expression patterns. Promoter sequence analysis reveals an enrichment of several cis-regulatory elements related to symbiosis, and modulation of plant gene expression during the interaction with microbes. Conclusions In conclusion, this study provides a comprehensive overview of the ARF gene family in chickpea. Globally, our data supports that auxin signaling pathway regulates a wide range of physiological processes and stress responses. Our findings could further provide new insights into the complexity of the regulation of ARF at the transcription level that may be useful to develop rational chickpea breeding strategies to improve development or stress responses. Our study also provides a foundation for comparative genomic analyses and a framework to trace the dynamic evolution of ARF genes on a large time-scale within the legume family. Electronic supplementary material The online version of this article (10.1186/s12864-018-4695-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jose V Die
- Department of Genetics, ETSIAM, University of Córdoba, Córdoba, Spain.
| | - Juan Gil
- Department of Genetics, ETSIAM, University of Córdoba, Córdoba, Spain
| | - Teresa Millan
- Department of Genetics, ETSIAM, University of Córdoba, Córdoba, Spain
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12
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Padhi BK, Singh M, Rosales M, Pelletier G, Cakmak S. A PCR-based quantitative assay for the evaluation of mRNA integrity in rat samples. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 15:18-23. [PMID: 29922590 PMCID: PMC6006387 DOI: 10.1016/j.bdq.2018.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 01/22/2023]
Abstract
Reverse Transcription quantitative real-time PCR (RT-qPCR) is applied to quantify gene transcript levels in a wide range of investigations. Proper assessment of RNA integrity is essential for reliable assessment of gene expression levels, as RNA molecules are acutely vulnerable to degradation. However, RNA quality control measures are still infrequently reported in rat toxicological studies, which impede proper evaluation of gene expression data reliability. The high operational cost of microfluidic capillary electrophoresis systems along with paucity of alternative methods for the quantitative assessment of rat RNA integrity constitute potential hurdles to the systematic implementation and reporting of RNA integrity assessment in rat studies. This manuscript describes the adaptation of an alternative RT-qPCR-based 3':5' assay as an additional option for the quantitative assessment of rat RNA integrity. Two PCR primer sets were designed on the 3' and 5' regions of a rat housekeeping gene to evaluate RNA integrity by measuring the relative expression (3':5' ratio) of these amplicons. The 3':5' ratios were then compared to Agilent Bioanalyzer's RNA integrity number (RIN) for a wide range of RNA samples originating from different tissues, cultured cell lines and rat strains that were prepared freshly, stored for years at -80 °C, purchased commercially or intentionally degraded. The 3':5' ratios and RIN values presented similar assessment of RNA integrity status from intact to heavily degraded samples. Based on the LOWESS regression of this large comparison dataset, 3':5' ratio threshold criteria equivalent to RIN cut-off values can be proposed for the selection of RNA samples for RT-qPCR analyses. This qPCR-based assay is easy to implement, cost-effective, and provides a reliable quantification of RNA integrity to assist in the selection of rat RNA samples suitable for downstream RT-qPCR gene expression analyses.
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Affiliation(s)
- Bhaja K. Padhi
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
- Corresponding author at: 50 Colombine driveway, P.L. 0803B, Ottawa, Ontario, K1A 0K9, Canada.
| | - Manjeet Singh
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Marianela Rosales
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Guillaume Pelletier
- Hazard Identification Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Sabit Cakmak
- Population Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
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13
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Buschmann D, Haberberger A, Kirchner B, Spornraft M, Riedmaier I, Schelling G, Pfaffl MW. Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow. Nucleic Acids Res 2016; 44:5995-6018. [PMID: 27317696 PMCID: PMC5291277 DOI: 10.1093/nar/gkw545] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
Small RNA-Seq has emerged as a powerful tool in transcriptomics, gene expression profiling and biomarker discovery. Sequencing cell-free nucleic acids, particularly microRNA (miRNA), from liquid biopsies additionally provides exciting possibilities for molecular diagnostics, and might help establish disease-specific biomarker signatures. The complexity of the small RNA-Seq workflow, however, bears challenges and biases that researchers need to be aware of in order to generate high-quality data. Rigorous standardization and extensive validation are required to guarantee reliability, reproducibility and comparability of research findings. Hypotheses based on flawed experimental conditions can be inconsistent and even misleading. Comparable to the well-established MIQE guidelines for qPCR experiments, this work aims at establishing guidelines for experimental design and pre-analytical sample processing, standardization of library preparation and sequencing reactions, as well as facilitating data analysis. We highlight bottlenecks in small RNA-Seq experiments, point out the importance of stringent quality control and validation, and provide a primer for differential expression analysis and biomarker discovery. Following our recommendations will encourage better sequencing practice, increase experimental transparency and lead to more reproducible small RNA-Seq results. This will ultimately enhance the validity of biomarker signatures, and allow reliable and robust clinical predictions.
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Affiliation(s)
- Dominik Buschmann
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Goethestraße 29, 80336 München, Germany
| | - Anna Haberberger
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Melanie Spornraft
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Irmgard Riedmaier
- Eurofins Medigenomix Forensik GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 München, Germany
| | - Gustav Schelling
- Department of Physiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
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14
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Galissier T, Schneider C, Nasri S, Kanagaratnam L, Fichel C, Coquelet C, Diebold MD, Kianmanesh R, Bellon G, Dedieu S, Marchal Bressenot A, Boulagnon-Rombi C. Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality? PLoS One 2016; 11:e0154326. [PMID: 27124490 PMCID: PMC4849710 DOI: 10.1371/journal.pone.0154326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/12/2016] [Indexed: 12/01/2022] Open
Abstract
Medical research projects become increasingly dependent on biobanked tissue of high quality because the reliability of gene expression is affected by the quality of extracted RNA. Hence, the present study aimed to determine if clinical, surgical, histological, and molecular parameters influence RNA quality of normal and tumoral frozen colonic tissues. RNA Quality Index (RQI) was evaluated on 241 adenocarcinomas and 115 matched normal frozen colon tissues collected between October 2006 and December 2012. RQI results were compared to patients’ age and sex, tumor site, kind of surgery, anastomosis failure, adenocarcinoma type and grade, tumor cell percentage, necrosis extent, HIF-1α and cleaved caspase-3 immunohistochemistry, and BRAF, KRAS and microsatellites status. The RQI was significantly higher in colon cancer tissue than in matched normal tissue. RQI from left-sided colonic cancers was significantly higher than RQI from right-sided cancers. The RNA quality was not affected by ischemia and storage duration. According to histological control, 7.9% of the samples were unsatisfactory because of inadequate sampling. Biobanked tumoral tissues with RQI ≥5 had lower malignant cells to stromal cells ratio than samples with RQI <5 (p <0.05). Cellularity, necrosis extent and mucinous component did not influence RQI results. Cleaved caspase-3 and HIF-1α immunolabelling were not correlated to RQI. BRAF, KRAS and microsatellites molecular status did not influence RNA quality. Multivariate analysis revealed that the tumor location, the surgical approach (laparoscopy versus open colectomy) and the occurrence of anastomotic leakage were the only parameters influencing significantly RQI results of tumor samples. We failed to identify parameter influencing RQI of normal colon samples. These data suggest that RNA quality of colonic adenocarcinoma biospecimens is determined by clinical and surgical parameters. More attention should be paid during the biobanking procedure of right-sided colon cancer or laparoscopic colectomy specimen. Histological quality control remains essential to control sampling accuracy.
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Affiliation(s)
- Thibaut Galissier
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
| | - Christophe Schneider
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Saviz Nasri
- Tumorothèque de Champagne Ardenne, Reims, France
| | - Lukshe Kanagaratnam
- Unité d’Aide Méthodologique, Centre Hospitalier Universitaire, Reims, France
| | - Caroline Fichel
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | | | - Marie-Danièle Diebold
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Tumorothèque de Champagne Ardenne, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Reza Kianmanesh
- Service de Chirurgie Digestive, Centre Hospitalier Universitaire, Reims, France
| | - Georges Bellon
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire de Biochimie, Centre Hospitalier Universitaire, Reims, France
| | - Stéphane Dedieu
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Aude Marchal Bressenot
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Camille Boulagnon-Rombi
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
- * E-mail:
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15
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Die JV, Roman B, Flores F, Rowland LJ. Design and Sampling Plan Optimization for RT-qPCR Experiments in Plants: A Case Study in Blueberry. FRONTIERS IN PLANT SCIENCE 2016; 7:271. [PMID: 27014296 PMCID: PMC4779984 DOI: 10.3389/fpls.2016.00271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
The qPCR assay has become a routine technology in plant biotechnology and agricultural research. It is unlikely to be technically improved, but there are still challenges which center around minimizing the variability in results and transparency when reporting technical data in support of the conclusions of a study. There are a number of aspects of the pre- and post-assay workflow that contribute to variability of results. Here, through the study of the introduction of error in qPCR measurements at different stages of the workflow, we describe the most important causes of technical variability in a case study using blueberry. In this study, we found that the stage for which increasing the number of replicates would be the most beneficial depends on the tissue used. For example, we would recommend the use of more RT replicates when working with leaf tissue, while the use of more sampling (RNA extraction) replicates would be recommended when working with stems or fruits to obtain the most optimal results. The use of more qPCR replicates provides the least benefit as it is the most reproducible step. By knowing the distribution of error over an entire experiment and the costs at each step, we have developed a script to identify the optimal sampling plan within the limits of a given budget. These findings should help plant scientists improve the design of qPCR experiments and refine their laboratory practices in order to conduct qPCR assays in a more reliable-manner to produce more consistent and reproducible data.
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Affiliation(s)
- Jose V. Die
- U.S. Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Belen Roman
- Area Mejora y Biotecnologia, IFAPA Centro Alameda del ObispoCordoba, Spain
| | - Fernando Flores
- Departamento Ciencias Agroforestales, Universidad de HuelvaHuelva, Spain
| | - Lisa J. Rowland
- U.S. Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
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16
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Simultaneous isolation of mRNA and native protein from minute samples of cells. Biotechniques 2014; 56:229-37. [PMID: 24806223 DOI: 10.2144/000114165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 03/04/2014] [Indexed: 11/23/2022] Open
Abstract
Precious biological samples often lack a sufficient number of cells for multiple procedures, such as extraction of mRNA while maintaining protein in a non-denatured state suitable for subsequent characterization. Here we present a new method for the simultaneous purification of mRNA and native proteins from samples containing small numbers of cells. Our approach utilizes oligodeoxythymidylate [oligo(dT)25]-coated paramagnetic beads in an optimized reaction buffer to isolate mRNA comparable in quantity and quality to mRNA isolated with existing methods, while maintaining the proteins in their native state for traditional protein assays. We validated the procedure using neonatal rat ovaries and small numbers of human granulosa cells, demonstrating the extraction of mRNA suitable for gene expression analysis with simultaneous isolation of native proteins suitable for downstream characterization using different protein assays.
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Die JV, Rowland LJ. Superior cross-species reference genes: a blueberry case study. PLoS One 2013; 8:e73354. [PMID: 24058469 PMCID: PMC3776805 DOI: 10.1371/journal.pone.0073354] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/18/2013] [Indexed: 11/28/2022] Open
Abstract
The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well.
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Affiliation(s)
- Jose V. Die
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Lisa J. Rowland
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
- * E-mail:
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18
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Die JV, Román B. RNA quality assessment: a view from plant qPCR studies. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6069-77. [PMID: 23045609 DOI: 10.1093/jxb/ers276] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) is probably the most common molecular technique used in transcriptome analyses today. The simplicity of the technology and associated protocols that generate results without the need to understand the underlying principles has made RT-qPCR the method of choice for RNA quantification. Rather than the 'gold standard technology' often used to describe it, the performance of RT-qPCR suffers from considerable pitfalls during general workflow. The inconsistency of conventional methods for the evaluation of RNA quality and its influence on qPCR performance as well as stability of reference genes is summarized and discussed here.
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Affiliation(s)
- Jose V Die
- Mejora Genética Vegetal, Instituto de Agricultura Sostenible, CSIC, 14080 Córdoba, Spain.
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