Massarray nanodispenser

Manufactured by Agena

Sourced in United States

The MassARRAY Nanodispenser is a laboratory instrument designed for high-precision liquid handling. It can accurately and consistently dispense small volumes of liquids, typically in the nanoliter range, for various applications in life science research and diagnostics.

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Lab products found in correlation

Massarray iplex platform, by Agena (4 mentions) Nanodrop 2000, by Thermo Fisher Scientific (4 mentions) Typer 4, by Agena (3 mentions) Nanodrop 2000 uv spectrophotometer, by Thermo Fisher Scientific (3 mentions) Massarray iplex, by Agena (2 mentions) Typer software version 4.0, by Agena (1 mentions) Nanodrop lite spectrophotometer, by Thermo Fisher Scientific (1 mentions) Massarray, by Labcorp (1 mentions) Spectrochip bioarray, by Agena (1 mentions) Massarray platform, by Agena (1 mentions) Assay design suite v2, by Agena (1 mentions)

10 protocols using massarray nanodispenser

STOX1 Genotyping by MassARRAY

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In this study, six SNPs (rs10998449, rs10762244, rs10998461, rs10998468, rs7903209, and rs4472827) in the STOX1 were selected from the DbSNP (

http://www.ncbi.nlm.nih.gov/projects/SNP/

) and 1,000 genome (

http://www.internationalgenome.org/

). All the SNPs were selected at a minor allele frequency >5% in Han Chinese from the 1,000 Genome Projects.
According to the manufacturer's protocol, GoldMag‐Mini Whole Blood Genomic DNA Purification Kit (GoldMag Co. Ltd.) was used to isolate the total genomic DNA from peripheral blood. The Agena Bioscience Assay Design Suite V2.0 software (http://agenacx.com/online-tools) was used to design the extended primer. The MassARRAY Nanodispenser (Agena Bioscience) and MassARRAY iPLEX platform (Agena Bioscience) were used to genotype, and the Agena Bioscience TYPER software (version 4.0) was used to analyze the data. We randomly selected about 10% of the sample to repeat genotyping, and the reproducibility was 100% indicating that our result is reliable.

Yang X., Li F., Xin D., Huang Z., Xue J., Wang B., Da Y., Xing W, & Zhu Y. (2019). Investigation of the STOX1 polymorphism on lumbar disc herniation. Molecular Genetics & Genomic Medicine, 8(1), e1038.

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Genotyping of SNPs with MassARRAY iPLEX

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Genomic DNA was extracted from peripheral blood using GoldMag‐Mini Whole Blood Genomic DNA Purification Kits (GoldMag Co. Ltd., Xi'an City, China), and quantified with a spectrophotometer (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA, United States). To have sufficient DNA for further reactions, polymerase chain reaction (PCR) was applied to each sample. Then SAP purification was performed to remove the remaining dNTP and amplified primers in PCR products. Using a MassARRAY Nanodispenser (Agena Bioscience, San Diego, CA), standardized genotyping reactions were dispensed onto a 384‐well spectroCHIP. The repeated control samples were set in every genotyping plate and the concordance was more than 99%. The genotyping of these SNPs was carried out on the MassARRAY iPLEX (Agena Bioscience, San Diego, CA) platform using the allele‐specific matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF‐MS). Genotyping results were outputted by Agena Bioscience TYPER 4.0. Haploview software package (version 4.2) was used to analyze the linkage disequilibrium (LD), haplotype construction, genetic association at polymorphism loci and haplotype blocks were defined according to the criteria laid out by Gabriel and others.25

Li M., Li A., He R., Dang W., Liu X., Yang T., Shi P., Bu X., Gao D., Zhang N., Du S., Jin T, & Chen M. (2019). Gene polymorphism of cytochrome P450 significantly affects lung cancer susceptibility. Cancer Medicine, 8(10), 4892-4905.

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Genotyping of ITPR2 Gene Variants

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Using the database of 1,000 Genomes Project (http://www.1000genomes.org/) and dbSNP (https://www.ncbi.nlm.nih.gov/SNP/), candidate SNPs in the ITPR2 gene with minor allele frequencies (MAFs)> 5% in the global population were selected. A total of eight SNPs (rs1049376, rs11048526, rs11048556, rs11048585, rs16931011, rs10842759, rs2230372, and rs7134213) were selected for further genotyping.
Peripheral blood samples (5 ml) were obtained from each participant. Genomic DNA was extracted from peripheral blood of cases and controls using the GoldMag‐Mini whole blood Genomic DNA Purification Kit (GoldMag Co. Ltd., Xi'an city, China), as recommended by the manufacturer's instructions (Geng et al., 2015). DNA concentration was determined by the NanoDrop Lite spectrophotometer (Thermo Fisher Scientific, Waltham, MA) (Wang et al., 2015). MassARRAY Nanodispenser (Agena Bioscience, San Diego, CA) was used to design primers for amplification process and single base extension reactions (Jin et al., 2015). SNP genotyping was carried out on the MassARRAY iPLEX (Agena Bioscience, SanDiego, CA) platform. Agena Bioscience Typer 4.0 software was used to manage and analyze SNP genotypic data.

He X., Bai M., Liu M., Wang L., He Y., Rong H., Yuan D, & Jin T. (2019). Genetic variants in the ITPR2 gene are associated with Kashin‐Beck Disease in Tibetan. Molecular Genetics & Genomic Medicine, 7(7), e00715.

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Genotyping Genetic Variants in Cervical Cancer

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rs11674595, rs4851527, rs719250, rs3218896, rs3218977, and rs2072472 in IL1R2 (GenBank reference sequence version number: NC_000002.12) were selected to be demonstrated in this study owing to their minor allele frequencies (MAF) >5% in Uygur women and Hardy–Weinberg equilibrium (HWE) p values >0.05 in controls. None of them has been reported previously in correlation to cervical cancer. Genomic DNA was extracted from blood samples with the GoldMag‐Mini Blood Genomic DNA Purification kit (GoldMagLtd., Xi'an, China). DNA concentration was measured at the wavelength of A260 nm by a NanoDrop 2000C spectrophotometer (Thermo Scientific, Waltham, MA, USA). Primers for multiplexed SNP MassEXTEND assay were designed with the application of Agena Bioscience Assay Design Suite software, version 2.0 (https://agenacx.com/online-tools/), and the genotypes of the SNPs were determined following the protocols of MassARRAY Nanodispenser (Agena Bioscience, San Diego, CA, USA) and MassARRAY iPLEX platform (Agena Bioscience) recommended by the manufacturer. Primers used in this study are listed in Supporting Information Table S1. Finally, Agena Bioscience TYPER software, version 4.0 was applied to conduct data management.

Niu F., Wang T., Li J., Yan M., Li D., Li B, & Jin T. (2018). The impact of genetic variants in IL1R2 on cervical cancer risk among Uygur females from China: A case–control study. Molecular Genetics & Genomic Medicine, 7(1), e00516.

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Genotyping of TNFAIP8L1 and FLT1 SNPs

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The total DNA isolation was performed from the peripheral blood samples provided by the experimental subjects using the GoldMag DNA Purification Kit (GoldMag Co. Ltd, Xi’an City, China). The concentration and quality of the purified DNA were measured with Nanodrop 2000 UV spectrophotometer (Thermo Scientific, Waltham, MA, U.S.A.). Screening the polymorphisms with minor allele frequency (MAF) more than 5% in the 1000 genomes database (http://www.internationalgenome.org/) and the dbSNP database (https://www.ncbi.nlm.nih.gov/projects/SNP/). We eventually selected five SNPs including rs9917028, rs10426502, and rs1060555 of TNFAIP8L1 and rs9513111 and rs677471 of FLT1 for further genotype identification and risk association analysis. The Agena Bioscience Assay Design Suite software, version 2.0 (https://agenacx.com/online-tools/) was applied for MassARRAY assay design. The SNP genotype was identified by the MassARRAY Nanodispenser and MassARRAY iPLEX method (Agena Bioscience, San Diego, CA, U.S.A.) according to the manufacturer’s instructions. Data management and presentation were conducted by the Agena Bioscience TYPER software, version 4.0 [17–19 (link)].

Han L., Husaiyin S., Ma C., Wang L, & Niyazi M. (2019). TNFAIP8L1 and FLT1 polymorphisms alter the susceptibility to cervical cancer amongst uyghur females in China. Bioscience Reports, 39(7), BSR20191155.

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Genotyping of NSE Gene SNPs

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Genomic DNA was extracted from the peripheral blood of each patient with the TIANGEN Kit (DP304, Beijing TIANGEN Biotechnology Co., Ltd.). The SNP genotyping method for all samples was based on the Sequenom MassARRAY® platform, and all amplification primers of the 6 NSE gene SNPs were designed according to the dbSNP database for sequencing and amplified by multiplex PCR to obtain site-specific PCR. The initial multiplex PCR amplification was performed using ABI Veriti-384 PCR. SAP (shrimp alkaline phosphatase) was used to remove the free dNTPs from the reaction system. After SAP treatment, the extended mixture was added in the abovementioned PCR system, to carry out single-base extension reactions, and then, a resin purification was conducted. Finally, a MassARRAY Nanodispenser (Agena, Inc.) was used to transfer the PCR products to the 384-well SpectroCHIP® bioarray. The genotypes and alleles were detected by the mass spectrometer MassARRAY Analyzer 4.0 and analyzed by the mass spectrometer MassARRAY TYPER4.0. According to the results of the analyses, the 6 SNPs were separately genotyped in all the samples.

Xu L., Liu X., Zhao J., Zeng J., Gu J., Zhang X., Zhang F., Han Y., Li W., Zhang P, & Gu R. (2020). Association between Neuron-Specific Enolase Gene Polymorphism and Delayed Encephalopathy after Acute Carbon Monoxide Poisoning. Behavioural Neurology, 2020, 8819210.

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Genotyping of GHR and PLCE1 variants

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We selected rs6898743 in GHR (NG_011688.2) and rs2274223 in PLCE1 (NG_015799.1) from the 1000 Genomes Project data (http://www.internationalgenome.org/) to analysis with minor allele frequency (MAF) >5%. DNA extraction from whole‐blood samples and DNA concentration were conducted based on the related literature report (Geng et al., 2015). MassARRAY Nanodispenser (Agena Bioscience, San Diego, CA, USA) was used to design primers (Jin et al., 2015). The sequences of primers were listed in Table S1. Genotyping was measured by MassARRAY platform (Agena Bioscience, San Diego, CA, USA) with a standard protocol. Data processing and analysis were performed by Agena Bioscience TYPER 4.0.

Wang R., Si L., Zhu D., Shen G., Long Q, & Zhao Y. (2020). Genetic variants in GHR and PLCE1 genes are associated with susceptibility to esophageal cancer. Molecular Genetics & Genomic Medicine, 8(10), e1474.

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FKBP5 Gene SNP Selection and Genotyping

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Haploview v.4.2 was used to select tagSNPs in linkage disequilibrium (LD) (r² > 0.8) with the remaining SNPs at minor allele frequency (MAF) > 0.1 in Han Chinese in Beijing (CHB). Functional SNP (rs3800373 and rs2817035) and SNPs most commonly associated with depressive symptoms or depressive disorder from the literature (rs7748266, rs9470080, rs4713902, rs1360780, rs9380524, rs9394309, rs7757037, rs1043805, rs2766533, rs4713916, rs9296158, rs2817032) [8 (link)–11 (link)] were prioritized as tagSNPs. In total, 14 SNPs were selected (Table S1). Assay Design 4.0 software (Agena Bioscience, Inc., San Diego, CA, USA) was used to design the primers. SNP genotyping was determined following the MassARRAY Nanodispenser (Agena Bioscience) protocols and MassARRAYiPLEX platform (Agena Bioscience) recommended by the manufacturer. None of the selected SNPs had more than 10% genotyping errors or were in severe Hardy-Weinberg disequilibrium (P < 0.001). Moreover, LD between the selected polymorphisms of the FKBP5 gene was examined by pair-wise comparisons of D′ and r² using Haploview v.4.2. One LD block (consisting of the SNPs rs9380524, rs7748266, rs1360780, and rs4713902; r² = 0.08–0.79) were identified and presented in Fig. S1 (relatively low LD).

Guo L., Wang W., Guo Y., Du X., Shi G, & Lu C. (2021). Associations of FKBP5 polymorphisms and methylation and parenting style with depressive symptoms among Chinese adolescents. BMC Psychiatry, 21, 552.

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Genotyping TERT Gene Variants

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Using the public HapMap databases, we randomly selected five SNPs on the basis of their allele frequencies, location, and disease relevance etc. All SNPs in TERT (GenBank: NG_009265.1) which have been validated with minor allele frequency (MAF)> 5% in the 1,000 genome (http://www.internationalgenome.org/). A total of five SNPs in the TERT gene were selected for further genotyping.
We collected the subjects about 5 ml of venous blood in EDTA tubes and stored in a −80℃ refrigerator. Extraction of genomic DNA from peripheral blood using the E.Z.N.A. ® Blood Mini Kit II (Omega Bio‐tek, Inc, USA), and then concentration was detected by the NanoDrop 2000 (Thermo Scientific, Waltham, MA, USA). Genotyping of all SNPs was performed using MassARRAY Nanodispenser (Agena Bioscience, San Diego, CA, USA and MassARRAY iPLEX platform (Agena Bioscience, San Diego, CA, USA), the experimental procedure was performed according to the manufacturer's protocol (Gabriel, Ziaugra, & Tabbaa, 2009). Primers and multiplex reactions were designed using the Agena Bioscience Assay Design Suite V2.0 software (https://agenacx.com/online-tools/), the corresponding primer for each SNPs is shown in Table 1. Data management and analysis were performed using Sequenom Typer 4.0 software (Gabriel et al., 2009; Thomas et al., 2007).

Ding Y., Li Q., Wu C., Wang W., Zhao J., Feng Q., Zhou X., Xie Y., Lin M., He P, & Xie P. (2019). TERT gene polymorphisms are associated with chronic obstructive pulmonary disease risk in the Chinese Li population. Molecular Genetics & Genomic Medicine, 7(8), e773.

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Genotyping of Cadherin Gene SNPs

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Genomic DNA was extracted from the peripheral blood using the TIANGEN kit (DP304, Beijing Tiangen Biotechnology Co., Ltd.). The Sequenom MassARRAY® platform was used to perform SNP genotyping of all the samples. First, the amplification primers required for the 4 SNP sites of cadherin according to the dbSNP database were designed and sequenced, and the site-specific PCR was obtained by multiplex PCR amplification. Then, ABI Veriti-384 PCR was used for the initial multiplex PCR amplification and extension. After resin purification, MassARRAY Nanodispenser (Agena, Inc.) was used to transfer the PCR products to a 384-well biochip. Finally, the genotype and alleles were detected by using the MassARRAY Analyzer 4.0 and analyzed by using MassARRAY TYPER4.0. As a result, 4 SNPs were genotyped in all samples.

Liu X., Zeng J., Zhang X., Gu J., Zhang F., Han Y., Zhang P., Li W, & Gu R. (2022). The Relationship between Cadherin Polymorphisms and the Risk of Delayed Encephalopathy after Acute Carbon Monoxide Poisoning in the Chinese Han Population. Behavioural Neurology, 2022, 3155703.

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