The Sequenom MassARRAY platform (CapitalBio, China) was used to perform quantitative methylation analysis of DAZ1-3 (GenBank accession number NC_000024.10). Detailed detection mechanisms were interpreted as described previously26 (link). PCR amplification was performed as follows: a hot start at 94 °C for 15 min; 45 cycles of denaturation at 94 °C for 20 s, annealing at 56 °C for 30 s, and extension at 72 °C for 1 min and a final incubation at 72 °C for 3 min. Then, 2 ml of premix including 0.3 U of SAP (Sequenom), was added to dephosphorylate the unincorporated dNTPs. The reaction mixture was incubated at 37 °C for 40 min. SAP was inactivated for 5 min at 85 °C before further treatment. The PCR mixture was used as a template for IVT, and RNase A cleavage was used as the reverse reaction. The mixture was conditioned and spotted on a 384-pad Spectro-CHIP (Sequenom) by a MassARRAY nanodispenser (Samsung, USA), followed by spectral acquisition on a MassARRAY Compact MALDI-TOF (Sequenom). Five CpG sites were examined in each DAZ member (15 CpG sites in total). The methylation ratios were analyzed by EpiTyper software v1.0 (Sequenom, https://www.epidesigner.com/ ) to generate quantitative results for each CpG site or an aggregate of multiple CpG sites.
Massarray nanodispenser
Manufactured by Samsung
Sourced in United States
The MassARRAY nanodispenser is a laboratory instrument designed for precise and automated liquid handling. It is capable of dispensing nanoliter-scale volumes with high accuracy and repeatability, making it suitable for a variety of applications in life science research and diagnostics.
Automatically generated - may contain errors
Lab products found in correlation
Spectrochip, by Labcorp (1 mentions)
Epityper software v1, by Labcorp (1 mentions)
Massarray compact maldi tof, by Labcorp (1 mentions)
Massarray platform, by Labcorp (1 mentions)
Mass array compact system, by Agena (1 mentions)
Massarray iplex platform, by Labcorp (1 mentions)
Maxwell 16, by Promega (1 mentions)
Maxwell 16 dna purification kit, by Promega (1 mentions)
3 protocols using massarray nanodispenser
1
Quantitative Methylation Analysis of DAZ Genes
2
Genotyping HIF2α Polymorphisms via MALDI-TOF MS
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For detection of HIF2α polymorphisms, 29 tag SNPs of HIF2α were genotyped by using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) as previously described (17 (link)). Genotyping was performed using MALDI-TOF MS (MassArray™ Nanodispenser, SAMSUNG). All reactions were designed in multiplexes of up to 29 tag SNPs usingAssay Design v2.0 software (Agena Bioscience). The data were collected using the Mass ARRAY Compact System (Agena Bioscience). Detailed primer information is provided in Supplementary Material 1
3
SNP Genotyping by Sequenom MassARRAY
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The following SNPs were studied: PNPLA3 (rs738409), TM6SF2 (rs58542926), MBOAT7 (rs641738), IL28B (rs12979860), TIMP-1 (rs4898), TIMP-2 (rs8179090), and NF-kB promoter (rs28362491).
Whole blood was used to extract DNA for SNP evaluation. Samples were frozen to -20°C until use. An aliquot of 400 µL was processed with the semi-automatic instrument Maxwell® 16 (Promega Corporation, Madison, WI USA), able to purify DNA from 16 samples simultaneously. DNA was purified with a specific kit (Maxwell 16 DNA Purification Kits, Promega Corporation, Madison, WI USA) and then quantified with the spectrophotometer Nanodrop 3.0.0. " (Celbio S.P.A, Milano, Italia). SNPs genotyping was performed in a 384 well-plate format on the Sequenom MassARRAY iPLEX platform (Sequenom, San Diego, USA). Primers were designed using the dedicated online software Assay Design v.4.0 (http://www.mysequenom.com, Sequenom Inc., San Diego, CA, USA). After the polymerase chain reaction, analytes were transferred from the plate to the microchip (SpectroCHIP bioarray®) using the MassARRAY Nanodispenser (Samsung). The loaded microchip was then put into the mass-spectrometer (MALDI-TOF; Matrix-Assisted Laser Desorption/Ionisation Time Of Flight; Sequenom Inc., San Diego, CA, USA) for analysis. Data acquisition occurred through dedicated software.
Whole blood was used to extract DNA for SNP evaluation. Samples were frozen to -20°C until use. An aliquot of 400 µL was processed with the semi-automatic instrument Maxwell® 16 (Promega Corporation, Madison, WI USA), able to purify DNA from 16 samples simultaneously. DNA was purified with a specific kit (Maxwell 16 DNA Purification Kits, Promega Corporation, Madison, WI USA) and then quantified with the spectrophotometer Nanodrop 3.0.0. " (Celbio S.P.A, Milano, Italia). SNPs genotyping was performed in a 384 well-plate format on the Sequenom MassARRAY iPLEX platform (Sequenom, San Diego, USA). Primers were designed using the dedicated online software Assay Design v.4.0 (http://www.mysequenom.com, Sequenom Inc., San Diego, CA, USA). After the polymerase chain reaction, analytes were transferred from the plate to the microchip (SpectroCHIP bioarray®) using the MassARRAY Nanodispenser (Samsung). The loaded microchip was then put into the mass-spectrometer (MALDI-TOF; Matrix-Assisted Laser Desorption/Ionisation Time Of Flight; Sequenom Inc., San Diego, CA, USA) for analysis. Data acquisition occurred through dedicated software.
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