Spectrochiparrays

Manufactured by Agena

Sourced in United States

SpectroChipArrays are a type of lab equipment designed for high-throughput spectroscopic analysis. They provide a platform for the simultaneous measurement of multiple analytes or samples using various spectroscopic techniques, such as absorbance, fluorescence, or Raman spectroscopy.

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Lab products found in correlation

Massarray system, by Agena (2 mentions) Nanodispenser, by Agena (2 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Spectrotyper v4, by Agena (1 mentions) Typer 4, by Agena (1 mentions) Iplex gold kit, by Agena (1 mentions) Applied biosystems geneamp pcr system 9700, by Thermo Fisher Scientific (1 mentions) Massarray 4 system, by Agena (1 mentions) Massarray typer software v4, by Agena (1 mentions) Shrimp alkaline phosphatase, by Agena (1 mentions)

4 protocols using spectrochiparrays

Mutation Detection in NSCLC Samples using OncoFOCUS Panel

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Mutation detection was performed in 18 LUAD and 20 LUSC stage IIIA NSCLC samples using the OncoFOCUS panel V1.0 (Includes various known hotspot mutations of EGFR, KRAS, NRAS, and BRAF) on the MassARRAY® System and Typer 4 software (Agena Bioscience, San Diego, CA, USA), which employs matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for amplicon detection. Briefly, PCR reactions for 45 cycles were set-up containing Taq DNA polymerase (Agena Bioscience), genomic DNA (20 ng), PCR primers, and dNTP. Following the PCR reaction, SAP addition, and iPLEX Pro extension reaction, the samples were desalted by resin treatment for 15 min, spotted onto SpectroCHIP® Arrays (Agena Bioscience, San Diego, CA), analyzed by MassARRAY® System, and ultimately interpreted on SpectroTYPER v4.0 software (Agena Bioscience, San Diego, CA).

Singh N., Mishra A., Sahu D.K., Jain M., Shyam H., Tripathi R.K., Shankar P., Kumar A., Alam N., Jaiswal R, & Kumar S. (2020). Comprehensive Characterization of Stage IIIA Non-Small Cell Lung Carcinoma. Cancer Management and Research, 12, 11973-11988.

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Genotyping Assays via IPLEX MassARRAY

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Genotyping was performed via IPLEX MassARRAY PCR using the Agena platform (Agena Bioscience, San Diego, CA, USA). IPLEX MassARRAY PCR and extension primers were designed from sequences containing each target SNP and 150 upstream and downstream bases with Assay Designer 4.0.0.2 (Agena Bioscience, San Diego, CA, USA) using the default settings. Single base extension reactions were performed on the PCR reactions with the iPLEX Gold Kit (Agena Bioscience) and 0.8 µL of the custom UEP pool. PCR reactions were dispensed onto SpectroChipArrays with a Nanodispenser (Agena Bioscience). An Agena Bioscience Compact MassArray Spectrometer was used to perform MALDI–TOF mass spectrometry according to the iPLEX Gold Application Guide. The Typer 4 software package (Agena Bioscience) was used to analyse the resulting spectra, and the composition of the target bases was determined from the mass of each extended oligo. These panels were designed in collaboration with PATIA, and genotyping was performed using the Agena platform located at the Epigenetics and Genotyping laboratory, Central Unit for Research in Medicine (UCIM), Faculty of Medicine, University of Valencia, Valencia, Spain.

Rodriguez-Carnero G., Lorenzo P.M., Canton-Blanco A., Mendizabal L., Arregi M., Zulueta M., Simon L., Macia-Cortiñas M., Casanueva F.F, & Crujeiras A.B. (2022). Genetic Variants in Folate and Cobalamin Metabolism-Related Genes in Pregnant Women of a Homogeneous Spanish Population: The Need for Revisiting the Current Vitamin Supplementation Strategies. Nutrients, 14(13), 2702.

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SNP Genotyping for Sample Identification

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DNA samples were normalized to 5–10 ng/μl, and identity test was performed using iPLEX^® Pro Sample ID Panel kit (Cat. No. 25094, Agena Bioscience, San Diego, CA). Multiplex-PCR targeting 44 identity SNPs was carried out in a 5-μl volume on an Applied Biosystems GeneAmp^® PCR System 9700 (Thermo Fisher Scientific, Waltham, MA) with the cycling program recommended by the manufacturer’s manual. After PCR, amplicons were treated with 5 U shrimp alkaline phosphatase (SAP; Agena Bioscience, San Diego, CA USA) and followed by adding 2 μl single-base extension (SBE) cocktail (Agena Bioscience, San Diego, CA) to continue the SBE reaction on a GeneAmp^® PCR System 9700 with the cycling program recommended by the manufacturer. SBE products were cleaned up using an ion-exchange resin and then spotted on SpectroCHIP arrays (Agena Bioscience, San Diego, CA USA). Raw data were acquired on a MassARRAY^® 4 system (Agena Bioscience, San Diego, CA USA) by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis. Genotypes for 44 SNPs were generated by MassARRAY Typer software v4.0 (Agena Bioscience, San Diego, CA).

Manheimer K.B., Richter F., Edelmann L.J., D’Souza S.L., Shi L., Shen Y., Homsy J., Boskovski M.T., Tai A.C., Gorham J., Yasso C., Goldmuntz E., Brueckner M., Lifton R.P., Chung W.K., Seidman C.E., Seidman J.G, & Gelb B.D. (2018). Robust identification of mosaic variants in congenital heart disease. Human genetics, 137(2), 183-193.

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SNP Genotyping of Biobank Samples

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DNA was isolated using the buffy coat obtained from one of the blood samples collected during the OGTT (K2-EDTA tubes). DNA concentration and purity were determined using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). A 16 Maxwell automated DNA extractor (Promega, Dübendorf, Switzerland) was used to extract DNA. SNP genotyping was performed using the MassARRAY system (Agena Bioscience, San Diego, CA, USA) combined with the iPLEX Gold SNP Genotyping method. PCR and iPLEX extension primers were designed using Assay Design Suite V2.0 online (Agena Bioscience, San Diego, CA, USA). The reaction products were transferred from the microplates into SpectroChipArrays with a Nanodispenser (Agena Bioscience). An Agena Bioscience MassARRAY Spectrometer was used to perform a MALDI-TOF–MS analysis. Genotyping results were analyzed via the MassArrayTyper 4.0 software. Panels were designed in collaboration with PATIA, and genotyping was performed at the Epigenetic and Genotyping Laboratory, Central Unit for Research in Medicine (UCLM), Faculty of Medicine, University of Valencia, Valencia, Spain. A comprehensive description of the genotyping methodology was previously published (https://doi.org/10.3389/fendo.2022.1036088, accessed on 29 January 2024).

Arnoriaga-Rodríguez M., Serrano I., Paz M., Barabash A., Valerio J., del Valle L., O’Connors R., Melero V., de Miguel P., Diaz Á., Familiar C., Moraga I., Pazos-Guerra M., Martínez-Novillo M., Rubio M.A., Marcuello C., Ramos-Leví A., Matia-Martín P, & Calle-Pascual A.L. (2024). A Simplified Screening Model to Predict the Risk of Gestational Diabetes Mellitus in Caucasian and Latin American Pregnant Women. Genes, 15(4), 482.

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