1
|
Đermić D, Ljubić S, Matulić M, Procino A, Feliciello MC, Ugarković Đ, Feliciello I. Reverse transcription-quantitative PCR (RT-qPCR) without the need for prior removal of DNA. Sci Rep 2023; 13:11470. [PMID: 37454173 PMCID: PMC10349872 DOI: 10.1038/s41598-023-38383-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
The procedure illustrated in this paper represents a new method for transcriptome analysis by PCR (Polymerase Chain Reaction), which circumvents the need for elimination of potential DNA contamination. Compared to the existing methodologies, our method is more precise, simpler and more reproducible because it preserves the RNA's integrity, does not require materials and/or reagents that are used for elimination of DNA and it also reduces the number of samples that should be set up as negative controls. This novel procedure involves the use of a specifically modified primer during reverse transcription step, which contains mismatched bases, thus producing cDNA molecules that differ from genomic DNA. By using the same modified primer in PCR amplification, only cDNA template is amplified since genomic DNA template is partially heterologous to the primer. In this way, amplification by PCR is unaffected by any potential DNA contamination since it is specific only for the cDNA template. Furthermore, it accurately reflects the initial RNA concentration of the sample, which is prone to changes due to various physical or enzymatic treatments commonly used by the current methodologies for DNA elimination. The method is particularly suitable for quantification of highly repetitive DNA transcripts, such as satellite DNA.
Collapse
Affiliation(s)
- Damir Đermić
- Division of Molecular Biology, Ruder Boskovic Institute, 10000, Zagreb, Croatia
| | - Sven Ljubić
- Division of Molecular Biology, Ruder Boskovic Institute, 10000, Zagreb, Croatia
| | - Maja Matulić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Alfredo Procino
- Division of Molecular Biology, Ruder Boskovic Institute, 10000, Zagreb, Croatia
| | - Maria Chiara Feliciello
- Department of Statistical Science, Alma Mater Studiorum, University of Bologna, 40126, Bologna, Italy
| | - Đurđica Ugarković
- Division of Molecular Biology, Ruder Boskovic Institute, 10000, Zagreb, Croatia.
| | - Isidoro Feliciello
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80135, Naples, Italy.
| |
Collapse
|
2
|
Li X, Zhang P, Wang H, Yu Y. Genes expressed at low levels raise false discovery rates in RNA samples contaminated with genomic DNA. BMC Genomics 2022; 23:554. [PMID: 35922750 PMCID: PMC9351092 DOI: 10.1186/s12864-022-08785-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022] Open
Abstract
Background RNA preparations contaminated with genomic DNA (gDNA) are frequently disregarded by RNA-seq studies. Such contamination may generate false results; however, their effect on the outcomes of RNA-seq analyses is unknown. To address this gap in our knowledge, here we added different concentrations of gDNA to total RNA preparations and subjected them to RNA-seq analysis. Results We found that the contaminating gDNA altered the quantification of transcripts at relatively high concentrations. Differentially expressed genes (DEGs) resulting from gDNA contamination may therefore contribute to higher rates of false enrichment of pathways compared with analogous samples lacking numerous DEGs. A strategy was developed to correct gene expression levels in gDNA-contaminated RNA samples, which assessed the magnitude of contamination to improve the reliability of the results. Conclusions Our study indicates that caution must be exercised when interpreting results associated with low-abundance transcripts. The data provided here will likely serve as a valuable resource to evaluate the influence of gDNA contamination on RNA-seq analysis, particularly related to the detection of putative novel gene elements. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08785-1.
Collapse
Affiliation(s)
- Xiangnan Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Haijian Wang
- Shanghai Pudong Hospital, Ministry of Education Key Laboratory of Contemporary Anthropology and Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Ying Yu
- Human Phenome Institute, Fudan University, Shanghai, China.
| |
Collapse
|
3
|
A bioinformatics framework for targeted gene expression assay design: Application to in vitro developmental neurotoxicity screening in a rat model. Regul Toxicol Pharmacol 2022; 133:105211. [PMID: 35724854 DOI: 10.1016/j.yrtph.2022.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/05/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022]
Abstract
Brain development involves a series of intricately choreographed neuronal differentiation and maturation steps that are acutely vulnerable to interferences from chemical exposures. Many genes involved in neurodevelopmental processes show evolutionarily conserved expression patterns in mammals and may constitute useful indicators/biomarkers for the evaluation of potential developmental neurotoxicity. Based on these premises, this study developed a bioinformatics framework to guide the design of a gene expression-based in vitro developmental neurotoxicity assay targeting evolutionary conserved genes associated with neuronal differentiation and maturation in rat cerebellar granule cells (CGCs). Rat, mouse and human genes involved in neurodevelopment and presenting one-to-one orthology were selected and orthologous exons within these genes were identified. PCR primer sets were designed within these orthologous exons and their specificity was evaluated in silico. The performance and specificity of rat, mouse and human PCR primer sets were then confirmed experimentally. Finally, RT-qPCR analyses in CGCs exposed in vitro to well-known neurotoxicants (Chlorpyrifos and Chlorpyrifos oxon) uncovered perturbations of expression levels for most of the selected genes. This bioinformatics framework for gene and target sequence selection may facilitate the identification of transcriptional biomarkers for developmental neurotoxicity assays and the comparison of gene expression data across experimental models from different mammalian species.
Collapse
|
4
|
Jiang Z, Xia W, Dai G, Zhang B, Li Y, Chen X. MicroRNA miR-4709-3p targets Large Tumor Suppressor Kinase 2 (LATS2) and induces obstructive renal fibrosis through Hippo signaling. Bioengineered 2021; 12:12357-12371. [PMID: 34931960 PMCID: PMC8810092 DOI: 10.1080/21655979.2021.2002493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
Obstructive renal fibrosis is the consequence of abnormal extracellular matrix assembly, which eventually results in renal failure, acute, and end‑stage renal infection. MicroRNAs (miRNAs), a particular category of small RNAs, modulate the expression of genes post-transcriptionally and regulate biological activities, including fibrogenesis. The study probed to estimate the key functions of miR-4709-3p in obstructive renal fibrosis. This investigation used TGF-β1 stimulated HK-2 in-vitro model, unilateral ureteral occlusion (UUO) mice model, and human Diabetic nephropathy (DN) and Renal interstitial fibrosis (RIF) specimens to depict the abundance of the miR-4709-3p level using FISH and RT-qPCR. MiR-4709-3p mimics and inhibitors were utilized to evaluate the functions of miR-4709-3p in-vitro. Luciferase assay was exploited to verify miR-4709-3p and LATS2 3'UTR binding. Finally, to depict the functions of miR-4709-3p in-vivo, the UUO model was injected with miR-4709-3p inhibitors. Results exhibited the upregulation of miR-4709-3p in UUO-induced in-vivo model, TGF-β1 stimulated HK-2, and human RIF and DN samples. Moreover, it was determined that modulating miR-4709-3p regulated the level of fibrosis markers. Luciferase assay miR-4709-3p modulates renal fibrosis by targeting LATS2. Finally, it was found that miR-4709-3p regulates obstructive renal fibrosis through the Hippo signaling pathway. Overall, the study concludes that aberrant miR-4709-3p expression plays an essential function in the renal fibrosis progression, and miR-4709-3p overexpression could advance obstructive renal fibrosis via LATS2 targeting in Hippo signaling pathway. Therefore, miR-4709-3p inhibition may be a potential renal fibrosis therapy target.
Collapse
Affiliation(s)
- Zexiang Jiang
- Department of Urology Surgery, Xiangya Hospital Central South University, Changsha City, China
| | - Weiping Xia
- Department of Urology Surgery, Xiangya Hospital Central South University, Changsha City, China
| | - Guoyu Dai
- Department of Urology Surgery, Xiangya Hospital Central South University, Changsha City, China
| | - Bo Zhang
- Department of Urology Surgery, Xiangya Hospital Central South University, Changsha City, China
| | - Yang Li
- Department of Urology Surgery, Xiangya Hospital Central South University, Changsha City, China
| | - Xiang Chen
- Department of Urology Surgery, Xiangya Hospital Central South University, Changsha City, China
| |
Collapse
|
5
|
Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR. Methods Protoc 2020; 3:mps3020040. [PMID: 32456168 PMCID: PMC7359704 DOI: 10.3390/mps3020040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022] Open
Abstract
In transfection experiments with mammalian cells aiming to overexpress a specific protein, it is often necessary to correctly quantify the level of the recombinant and the corresponding endogenous mRNA. In our case, mouse calvarial osteoblasts were transfected with a vector containing the complete Pex11β cDNA (plasmid DNA). The Pex11β mRNA level, as calculated using the RT-qPCR product, was unrealistically higher (>1000-fold) in transfected compared to non-transfected cells, and we assumed that there were large amounts of contaminating plasmid DNA in the RNA sample. Thus, we searched for a simple way to distinguish between plasmid-derived mRNA, endogenous genome-derived mRNA and plasmid DNA, with minimal changes to standard RT-PCR techniques. We succeeded by performing a plasmid mRNA-specific reverse transcription, and the plasmid cDNA was additionally tagged with a nonsense tail. A subsequent standard qPCR was conducted using appropriate PCR primers annealing to the plasmid cDNA and to the nonsense tail. Using this method, we were able to determine the specific amount of mRNA derived from the transfected plasmid DNA in comparison to the endogenous genome-derived mRNA, and thus the transfection and transcription efficiency.
Collapse
|
6
|
A bioinformatics workflow for the evaluation of RT-qPCR primer specificity: Application for the assessment of gene expression data reliability in toxicological studies. Regul Toxicol Pharmacol 2020; 111:104575. [PMID: 31945455 DOI: 10.1016/j.yrtph.2020.104575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
The reliability of Reverse Transcription quantitative real-time PCR (RT-qPCR) gene expression data depends on proper primer design and RNA quality controls. Despite freely available genomic databases and bioinformatics tools, primer design deficiencies can be found across life science publications. In order to assess the prevalence of such deficiencies in the toxicological literature, 504 primer sets extracted from a random selection of 70 recent rat toxicological studies were evaluated. The specificity of each primer set was systematically analysed using a bioinformatics workflow developed from publicly available resources (NCBI Primer BLAST, in silico PCR in UCSC genome browser, Ensembl DNA database). Potential mismatches (9%), cross-matches (13.5%), co-amplification of multiple gene splice variants (9%) and sub-optimal amplicon sizes (25%) were identified for a significant proportion of the primer sets assessed in silico. Quality controls for gDNA contamination of RNA samples were infrequently reported in the surveyed manuscripts. Hence, the impacts of gDNA contamination on RT-qPCR data were further investigated, revealing that lowly expressed genes presented higher susceptibility to contaminating gDNA. In addition to the retrospective identification of potential primer design issues presented in this study, the described bioinformatics workflow can also be used prospectively to select candidate primer sets for experimental validation.
Collapse
|
7
|
Isolation of DNA-free RNA from human bone marrow mononuclear cells: comparison of laboratory methods. Biotechniques 2019; 68:159-162. [PMID: 31870171 DOI: 10.2144/btn-2019-0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
RNA quality (purity and integrity) and quantity are of critical importance to ensure reliable gene expression analysis, reproducibility of RNA sequencing and microarray data and validation by RT-PCR. Currently available methods for isolating RNA either are labor intensive (requiring the use of toxic organic solvents and separate DNase treatment) or require automation (with extensive setup and startup costs). To optimize both the quality and quantity of RNA from bone marrow, we recommend stabilization and storage of bone marrow mononuclear cells in RNAprotect® Cell Reagent, followed by extraction using the RNeasy® Protect Cell Mini Kit (Qiagen, Hilden, Germany). This method achieves optimal quantity and high-quality RNA for sequencing and RT-PCR while remaining efficient and cost effective.
Collapse
|
8
|
Sensitive quantification of the intronless SOX11 mRNA from lymph nodes biopsies in mantle cell lymphoma. Leuk Res 2019; 78:1-2. [PMID: 30640013 DOI: 10.1016/j.leukres.2019.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/30/2018] [Accepted: 01/02/2019] [Indexed: 11/22/2022]
|
9
|
Kip Ç, Gülüşür H, Çelik E, Usta DD, Tuncel A. Isolation of RNA and beta-NAD by phenylboronic acid functionalized, monodisperse-porous silica microspheres as sorbent in batch and microfluidic boronate affinity systems. Colloids Surf B Biointerfaces 2018; 174:333-342. [PMID: 30472619 DOI: 10.1016/j.colsurfb.2018.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 12/18/2022]
Abstract
Monodisperse-porous silica microspheres 5.5 μm in size were obtained by a staged shape templated hydrolysis-condensation method, with a bimodal pore-size distribution. 3-aminophenylboronic acid (APBA) was covalently attached onto the silica microspheres with a capacity of 0.476 mmol APBA/g microspheres. The boronate affinity isolation behaviour of ribonucleic acid (RNA) containing cis-diol at 3'-end was investigated by using APBA attached-silica microspheres as the sorbent in batch fashion. A short-chain diol carrying agent, β-nicotinamide adenine dinucleotide (β-NAD) was used as a target molecule with stronger affinity for phenylboronic acid ligand. The maximum equilibrium adsorptions for RNA and β-NAD were determined as 60 and 159 mg/g sorbent, respectively. By using the synthesized sorbent, phosphate buffer at pH 7.0 containing sorbitol was successfuly used as a mild elution medium for obtaining quantitative desorptions with both RNA and β-NAD. RNA isolations from mammalian and bacterial cells were successfully performed while protecting the structural integrity of RNA via boronate affinity interaction in batch fashion. A microfluidic boronate affinity system including a microcolumn 300 μm in diameter was also constructed using APBA attached-silica microspheres as the stationary phase. The breakthrough curves of microfluidic system were obtained by studying with different feed concentrations of RNA and β-NAD. Quantitative desorptions and satisfactory isolation yields were obtained with RNA and β-NAD in the microfluidic system. The proposed system is useful for boronate affinity applications in genomics or proteomics in which valuable cis-diols at low concentrations are recovered from low-volume samples.
Collapse
Affiliation(s)
- Çiğdem Kip
- Hacettepe University, Chemical Engineering Department, 06800, Ankara, Turkey
| | - Hilal Gülüşür
- Hacettepe University, Institute of Science, Division of Nanotechnology and Nanomedicine, 06800, Ankara, Turkey
| | - Eda Çelik
- Hacettepe University, Chemical Engineering Department, 06800, Ankara, Turkey; Hacettepe University, Institute of Science, Division of Bioengineering, 06800, Ankara, Turkey
| | - Duygu Deniz Usta
- Department of Medical Biology and Genetics, Gazi University, 06500, Ankara, Turkey; Department of Medical Biology, Istanbul Medeniyet University, 34700, Istanbul, Turkey
| | - Ali Tuncel
- Hacettepe University, Chemical Engineering Department, 06800, Ankara, Turkey.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Hashemipetroudi SH, Nematzadeh G, Ahmadian G, Yamchi A, Kuhlmann M. Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA. J Vis Exp 2018. [PMID: 29443017 PMCID: PMC5908672 DOI: 10.3791/55451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
One method extensively used for the quantification of gene expression changes and transcript abundances is reverse-transcription quantitative real-time PCR (RT-qPCR). It provides accurate, sensitive, reliable, and reproducible results. Several factors can affect the sensitivity and specificity of RT-qPCR. Residual genomic DNA (gDNA) contaminating RNA samples is one of them. In gene expression analysis, non-specific amplification due to gDNA contamination will overestimate the abundance of transcript levels and can affect the RT-qPCR results. Generally, gDNA is detected by qRT-PCR using primer pairs annealing to intergenic regions or an intron of the gene of interest. Unfortunately, intron/exon annotations are not yet known for all genes from vertebrate, bacteria, protist, fungi, plant, and invertebrate metazoan species. Here we present a protocol for detection of gDNA contamination in RNA samples by using ribosomal DNA (rDNA)-based primers. The method is based on the unique features of rDNA: their multigene nature, highly conserved sequences, and high frequency in the genome. Also as a case study, a unique set of primers were designed based on the conserved region of ribosomal DNA (rDNA) in the Poaceae family. The universality of these primer pairs was tested by melt curve analysis and agarose gel electrophoresis. Although our method explains how rDNA-based primers can be applied for the gDNA contamination assay in the Poaceae family, it could be easily used to other prokaryote and eukaryote species
Collapse
Affiliation(s)
- Seyyed Hamidreza Hashemipetroudi
- Genetic and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)
| | - Ghorbanali Nematzadeh
- Genetic and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetics Engineering and Biotechnology (NIGEB)
| | - Ahad Yamchi
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences & Natural Resources
| | - Markus Kuhlmann
- RG Abiotic Stress Genomics/ RG Heterosis, Department Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK);
| |
Collapse
|
12
|
Analysis of Expression of CCN Family Genes in Skeletal Tissue-Derived Cells. Methods Mol Biol 2016. [PMID: 27734363 DOI: 10.1007/978-1-4939-6430-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The quantitative reverse transcription polymerase chain reaction or real-time PCR has become a routine technique for the detection and comparison of amounts of specific mRNA transcripts, done by measuring amplified levels of specific cDNAs. In this chapter, we provide our real-time RT-PCR experimental procedure using SYBR Green I for the quantitative analysis of CCN family gene expression. Especially, we describe the extraction and purification steps for RNA derived from mesenchymal cells, such as chondrocytes and osteoblasts that produce a large amount of extracellular matrix in detail.
Collapse
|