Massarray analyzer

Manufactured by Labcorp

Sourced in United States

The MassARRAY Analyzer is a laboratory instrument designed for high-throughput genetic analysis. It utilizes mass spectrometry technology to accurately determine the molecular mass of DNA and RNA molecules, enabling efficient genotyping and mutation detection.

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Lab products found in correlation

Epityper v1, by Labcorp (3 mentions) Massarray platform, by Labcorp (3 mentions) 384 pad spectrochip, by Labcorp (2 mentions) Assay design software, by Labcorp (1 mentions) Iplex chemistry, by Labcorp (1 mentions) Epidesigner, by Labcorp (1 mentions) Iplex gold assay, by Labcorp (1 mentions) Pcr clean kit, by Qiagen (1 mentions) Hifi hotstart readymix, by Roche (1 mentions) Abi 3730xl, by Thermo Fisher Scientific (1 mentions) Bigdye terminator v3.1 cycle sequencing kit, by Thermo Fisher Scientific (1 mentions) Qiaamp dna blood mini kit, by Qiagen (1 mentions) Spectrochip, by Labcorp (1 mentions) Epityper software v1, by Labcorp (1 mentions)

6 protocols using massarray analyzer

MTHFR Gene Variant Genotyping

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Five milliliter of venous blood was collected with ethylene diamine tetra acetic acid (EDTA) as anticoagulant. Genomic DNA was extract from peripheral blood leukocytes using the Helix Extraction System (Diatech) and the X-Tractor Gene (Corbett Robotics).
MTHFR C677T (rs1801133) and A1298C (rs1801131) were genotyped in a single reaction using a multiplexed single-nucleotide extension system (IPlex chemistry, Sequenom, San Diego, CA, USA) following the manufacturer’s instruction. The extended products were analyzed using the MassArray Analyzer (Sequenom). Locus-specific amplification and extension primers were designed using the Assay Design Software (Sequenom). The primers’ sequences were for MTHFR C677T: 5’-ACGTTGGATGCTTGAAGGAGAAGGTGTCTG-3’ (forward), 5’-ACGTTGGATGTGCATGCCTTCACAAAGCGG-3’ (reverse), 5’-GCGTGATGATGAAATCG-3’ (extension). For MTHFR A1298C: 5’-ACGTTGGATGTCTCCCGAGAGGTAAAGAAC (forward), 5’-ACGTTGGATGAGGAGCTGCTGAAGATGTGG-3’ (reverse), 5’-GAGGAGCTGACCAGTGAAG-3’ (extension).

Mazzuca F., Borro M., Botticelli A., Aimati L., Gentile G., Capalbo C., Maddalena C., Mazzotti E., Simmaco M, & Marchetti P. (2015). Effect of MTHFR Polymorphisms on Gastrointestinal Cancer Risk in Italy. World Journal of Oncology, 6(4), 394-397.

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Quantifying miR-375 Methylation Levels

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To quantify the methylation levels of the miR-375 CpG islands in clinical samples, the high-throughput MassARRAY platform (Sequenom, Inc., San Diego, CA, USA) was used. Briefly, bisulfite-treated DNA was amplified with primers for the miR-375 CpG islands. The primers were designed using EpiDesigner (Sequenom Inc.) and were as follows: Forward 5′-aggaagagagGGGTGGAGTATTTTTGTTTGTTG-3′ and reverse 5′-cagtaatacgactcactatagggagaaggctAAAAACATAATCCAAAACATCCTAAT-3′. The PCR products were spotted on a 384-pad SpectroCHIP (Sequenom, Inc.), followed by spectral acquisition on a MassARRAY Analyzer (Sequenom, Inc.). Methylation data of individual units (1–3 CpG sites per unit) were generated using EpiTyper v1.0.5 software (Sequenom, Inc.).

WANG X., CHANG X., LI J., YIN L, & SUN K. (2014). DNA methylation of microRNA-375 in impaired glucose tolerance. Experimental and Therapeutic Medicine, 8(3), 775-780.

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Genotyping FcγR Polymorphisms in Peripheral Blood

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Blood samples were collected before treatment. Archived peripheral blood mononuclear cells were used for DNA extraction with the QIAamp DNA blood mini kit (Qiagen). Nested polymerase chain reaction (PCR) was conducted to detect single-nucleotide polymorphisms in FcγRIIA and/or IIIA using the same primers as in a previous study.21 (link) PCR was carried out using the HiFi HotStart ReadyMix (KAPA Biosystems) and optimized protocols. The PCR products were purified using the PCR clean kit (Qiagen) and then sequenced on an ABI3730XL (Applied Biosystems) with the BigDye Terminator v3.1 Cycle Sequencing Kit. The PCR products of 110 samples were also analyzed on MassARRAY analyzer (Sequenom) with the iPLEX Gold assay (Sequenom) using primers, as in a previous study,21 (link) to identify the A559C polymorphism in FcγRIIIA and the A519G polymorphism in FcγRIIA.

Wang D.S., Wei X.L., Wang Z.Q., Lu Y.X., Shi S.M., Wang N., Qiu M.Z., Wang F.H., Wang R.J., Li Y.H, & Xu R.H. (2017). FcγRIIA and IIIA polymorphisms predict clinical outcome of trastuzumab-treated metastatic gastric cancer. OncoTargets and therapy, 10, 5065-5076.

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Methylation Analysis of PTEN Promoter

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The sequence of the CpG island (CGI) was identified using the UCSC genome browser (http://genome.ucsc.edu/), (chr10:89621773-89624128% GC = 58.1 and Obs/Exp CpG = 0.86). The target of the promoter region was 1 amplicon (Fig. 1 and Fig. 2), as previously reported.^{[12 (link)–14 (link)]} We designed 1 primer set for the methylation analysis of the PTEN promoter region by EpiDesigner software (http://epidesigner.com; Table 1). For the reverse primer, an additional T7 promoter tag was added for in vivo transcription, and a 10-mer tag was added to the forward primer to adjust for the melting temperature differences. The primers used in the present study specifically detected the promoter sequence of the PTEN gene rather than that of the PTEN pseudogene (Fig. 2).^{[15 (link)]}To quantitatively evaluate the promoter methylation of PTEN in Uyghur T2DM patients, the high-throughput MassARRAY platform (Sequenom, San Diego, CA) was used as previously described.^{[16 (link)]} Briefly, primers for the PTEN CGI were used to amplify bisulfite-treated DNA, and the PCR products were spotted on a 384-pad SpectroCHIP (Sequenom, San Diego, CA), followed by spectral acquisition on a MassARRAY Analyzer. The methylation data of individual units (1 to 3 CpG sites per unit) were generated by the EpiTyper v1.0.5 software (Sequenom, San Diego, CA).

Yin L., Cai W.J., Chang X.Y., Li J., Zhu L.Y., Su X.H., Yu X.F, & Sun K. (2018). Analysis of PTEN expression and promoter methylation in Uyghur patients with mild type 2 diabetes mellitus. Medicine, 97(49), e13513.

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Quantitative DNA Methylation Analysis of UHRF1 Gene

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Quantitative high-throughput DNA methylation analysis was done by MassARRAY system as described elsewhere [55 (link)], using Sequenom MassARRAY quantitative methylation analysis system. Briefly, genomic DNA was isolated and treated with bisulfite as described above. Bisulfite treated DNA was amplified using nested primers covering CpG sites within the UHRF1 gene, spanning from Chr19:4950704 to Chr19:4950993. The primer sequences are available upon request. After Shrimp Alkaline Phosphatase treatment, the PCR products were used as a template for in vitro transcription and RNase A Cleavage for the T-reverse reaction as per manufacturer's instructions (Sequenom hMC). The samples were desalted and spotted on a SpectroCHIP (Sequenom), followed by spectral acquisition on a MassARRAY Analyzer (Sequenom) at Einstein Epigenomics Core Facility. The resultant methylation calls were performed by the EpiTyper software v1.0 (Sequenom) to generate quantitative results for each CpG site.

Yu B., Russanova V.R., Gravina S., Hartley S., Mullikin J.C., Ignezweski A., Graham J., Segars J.H., DeCherney A.H, & Howard B.H. (2015). DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3ʹ-end GC density. Oncotarget, 6(6), 3627-3643.

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Quantifying miR-375 CpG Methylation via MassARRAY

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To quantify methylation levels of the miR-375 CpG islands in the clinical samples, the high-throughput MassARRAY platform (Sequenom, San Diego, USA) was carried out as described previously [10 (link)]. Briefly, primers for the miR-375 CpG island were used to amply bisulfite treated DNA and then the PCR products were spotted on a 384-pad SpectroCHIP (Sequenom, San Diego, USA), followed by spectral acquisition on a MassARRAY Analyzer. Methylation data of individual units (one to three CpG sites per unit) were generated by the EpiTyper v1.0.5 software (Sequenom, San Diego, USA).

Chang X., Li S., Li J., Yin L., Zhou T., Zhang C., Chen X, & Sun K. (2014). Ethnic Differences in MicroRNA-375 Expression Level and DNA Methylation Status in Type 2 Diabetes of Han and Kazak Populations. Journal of Diabetes Research, 2014, 761938.

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