Ms200 scanner

Manufactured by Roche

Sourced in France

The MS200 scanner is a compact and versatile laboratory instrument designed for high-performance chromatographic analysis. It features a robust and reliable design, providing accurate and reproducible results. The MS200 scanner is capable of performing both qualitative and quantitative analyses, making it a valuable tool for a wide range of applications in the scientific and research community.

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MS200 microarray scanner (13 citations) NimbleGen MS200 scanner (13 citations) MS200 (3 citations)

13 protocols using ms200 scanner

RNA Isolation and Microarray Analysis Protocol

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Biopsies stored at −80°C in RNAlater were used for the isolation of total RNA with the
RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. RNA was
quantified by absorbance at 260/280 nm, and quality was evaluated using an Agilent 2100
Bioanalyzer and the RNA 6000 NanoChip kit (Agilent Technologies, Santa Clara, California).
Double-stranded complementary DNA (ds-cDNA) was generated from 5 µg of RNA using the cDNA
Synthesis Kit System (Roche Applied Science, Indianapolis, Indiana) and purified with the
GenElute polymerase chain reaction (PCR) Clean-up Kit (Sigma-Aldrich Quimica, Toluca,
Mexico). Afterward, the ds-cDNA was labeled with Cy3 and hybridized in a Human Gene
Expression Array 12 × 135 k (Roche Applied Science). Finally, the microarrays were scanned
on an MS200 Scanner (Roche Applied Science), and the data obtained were processed using
the DEVA 1.2 software (Roche Applied Science). Fluorescence intensities were normalized
using the RMA algorithm, and all data obtained were subsequently analyzed using the CLC
Main WorkBench version 7.0.3 software (Qiagen). Intensities of sensitive versus resistant
samples were compared and the genes were considered differentially expressed when the
intensities showed a difference of >1.5 and a P value <.05.

Garcia-Chagollan M., Carranza-Torres I.E., Carranza-Rosales P., Guzmán-Delgado N.E., Ramírez-Montoya H., Martínez-Silva M.G., Mariscal-Ramirez I., Barrón-Gallardo C.A., Pereira-Suárez A.L., Aguilar-Lemarroy A, & Jave-Suárez L.F. (2018). Expression of NK Cell Surface Receptors in Breast Cancer Tissue as Predictors of Resistance to Antineoplastic Treatment. Technology in Cancer Research & Treatment, 17, 1533033818764499.

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Microarray Hybridization and Scanning Protocol

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For each sample, 1650 ng of labeled and amplified cRNA was used for hybridization. The hybridization master mix was prepared according to manufacturer’s protocol (Agilent Technologies, Massy, France) and 100 μl were deposited onto a gasket slide, according to the Agilent Microarray Hybridization Chamber User Guide. Next, the active side of the microarray slide was placed on top of the gasket to form a properly aligned “sandwich slide pair”. The microarray slides were inserted into an Agilent Technology hybridization chamber then placed at 65 °C for 17 h with rotation at 10 rpm. After hybridization, the microarray was washed over a 1-min period, first using Gene Expression Wash Buffer 1 and then Gene Expression Wash Buffer 2 (Agilent Technologies, Massy, France) pre-warmed at 37 °C. After washing, the arrays were immediately scanned using an MS200 scanner (NimbleGen Roche Diagnostics, Meylan, France) with NimbleGen MS200 software v1.2 at 2 micron resolution.

Abot A., Arnal G., Auer L., Lazuka A., Labourdette D., Lamarre S., Trouilh L., Laville E., Lombard V., Potocki-Veronese G., Henrissat B., O’Donohue M., Hernandez-Raquet G., Dumon C, & Leberre V.A. (2016). CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems. BMC Genomics, 17(1), 671.

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Probe Labeling and Hybridization for Mouse Gene Expression

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Probe labelling and hybridization were performed with Roche NimbleGen kit using the standard protocol for eukaryotic RNA samples and NimbleGen mouse gene expression 12x135K array (Roche, cat. no. 05543797001). The cDNA samples were labelled with Cy3 using a NimbleGen One-Color DNA labelling kit (Roche, cat. no. 06370411001) and hybridized to slides using a NimbleGen hybridization system (Roche, cat. no. 05583683001). The slides were scanned using MS200 Scanner (Roche, NimbleGen) at 2 μm resolution by using high-sensitivity and autogain settings.

Podolak-Popinigis J., Górnikiewicz B., Ronowicz A, & Sachadyn P. (2015). Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse. BMC Genomics, 16, 926.

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Microarray Data Analysis Pipeline

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Cy5 fluorescence intensity of the arrays was measured with an MS200 scanner (Roche NimbleGen, Madison, WI) at resolution 2 µm, wavelength 635 nm, gain 25%, and laser intensity 100%. Cy5 signal intensities were extracted using Image Extraction Software (Roche NimbleGen). Data pre-processing, normalization, and statistical tests were performed using the language R. Data visualization and analysis was performed with the Spotfire 6.5.0 (Tibco, Boston, MA) software platform. Distance analysis and principle component analysis of distance matrices were performed with the R package PEPLIB^{19 (link)}.

Lyamichev V.I., Goodrich L.E., Sullivan E.H., Bannen R.M., Benz J., Albert T.J, & Patel J.J. (2017). Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target. Scientific Reports, 7, 12116.

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Genome-wide CNV Profiling by aCGH

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CNVs were mapped genome-wide to hg18 in all samples by aCGH using the NimbleGen 2.1 M CNV array (Roche NimbleGen) followed by analysis in Nexus Copy Number 6 (Biodiscovery) and NimbleScan 2.6 (Roche NimbleGen). Genomic DNA from each sample was labeled with cy3 dye and genomic DNA from a control pool of seven female individuals (Promega) was labeled using cy5 dye according to the NimbleGen CGH protocol. 34 μg of test and control DNA were mixed together and hybridized to an array for 60–72 hrs. The arrays were washed using the NimbleGen Wash kit and scanned using the MS 200 scanner (Roche NimbleGen) in two channels: 532 nm and 635 nm. Images were normalized using NimbleScan 2.6 (NS). Normalized data were used to derive LRRs using two algorithms: NimbleScan 2.6 segMNT algorithm (default parameters) and Nexus Copy Number 6.0 Rank Segmentation algorithm (significance threshold = 1.0^-9). Data were loaded into Nexus 6.0 and copy number calls were generated genome-wide for each sample based on fixed thresholds for deletions and duplications specified in the settings.

Haraksingh R.R., Jahanbani F., Rodriguez-Paris J., Gelernter J., Nadeau K.C., Oghalai J.S., Schrijver I, & Snyder M.P. (2014). Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss. BMC Genomics, 15(1), 1155.

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Exon-level Copy Number Analysis of Mutation Negative Cases

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In 33 mutation negative cases from phase 1, we performed exon-level copy number analysis using a custom Roche Nimblegen oligonucleotide 135K aCGH (see online supplementary table S1). Arrays were designed using proprietary Nimblegen software and read using a Roche Nimblegen MS 200 scanner. We analysed array data using CGH Fusion (infoQuant). We confirmed copy number abnormalities and performed segregation analysis in parental lymphocyte DNA samples using multiplex ligation-dependent probe amplification (MLPA) and/or FISH.

Trump N., McTague A., Brittain H., Papandreou A., Meyer E., Ngoh A., Palmer R., Morrogh D., Boustred C., Hurst J.A., Jenkins L., Kurian M.A, & Scott R.H. (2016). Improving diagnosis and broadening the phenotypes in early-onset seizure and severe developmental delay disorders through gene panel analysis. Journal of Medical Genetics, 53(5), 310-317.

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S. pneumoniae Whole Genome Expression Profiling

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High density Streptococus pneumoniae expression arrays from Agilent were processed at the Functional Genomics Core Facility, Institut de Recerca Biomèdica, Barcelona. Arrays were designed including 1 or 2 copies of 17 oligonucleotide probes (average size of 60 nucleotides) for each 2,037 protein coding genes from S. pneumoniae R6. cDNA library preparation and amplification was performed from 10 ng of R6 genomic DNA using WGA2 (Sigma Aldrich) with 10 cycles amplification. Labelling of 250 ng of cDNAs with Cy3 was performed by ULS. Hybridization was made following the Agilent Oligo Array-based CGH for genomic DNA analysis ULS protocol. Microarrays were scanned on a Roche MS200 scanner at 2 µm resolution and raw data were extracted using Feature Extraction software v11.5. Raw data were RMA normalized using Partek Genomics suite 6.5 (6.11.0207). The median of each group of 17 probes in each block of the array were considered. Each microarray experiment was carried out in duplicate.

Ferrándiz M.J., Arnanz C., Martín-Galiano A.J., Rodríguez-Martín C, & de la Campa A.G. (2014). Role of Global and Local Topology in the Regulation of Gene Expression in Streptococcus pneumoniae. PLoS ONE, 9(7), e101574.

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Genome-Wide Copy Number Analysis

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Genomic DNA was isolated from all 26 samples using a commercially available DNA extraction kit (Puregene blood kit, QIAGEN Inc., Valencia, CA). The manufacturer's protocol was followed on a 720k oligonucleotides chip purchased from Roche/NimbleGen System Inc. (Madison, WI). Commercially available pooled normal control DNA was used for reference (Promega Corporation, Madison, WI). The patient DNA and the reference DNA were labeled with either Cyanine 3 (Cy-3) or Cyanine 5 (Cy-5) by random priming (Trilink Biotechnologies, San Diego, CA) and then hybridized to the chip via incubation in the MAUI hybridization system (BioMicro Systems, Salt Lake City, UT). After the 40-hour hybridization at 42°C, the slides were washed and scanned using a MS200 scanner (Roche NimbleGen System Inc., Madison, WI). NimbleScan version 2.4 and the SignalMap version 1.9 were applied for data analysis (NimbleGen System Inc, Madison, WI). The genomic locations were retrieved from the National Center for Biotechnology Information (NCBI) build 36 (hg 18). Frequently affected regions recently detected as copy number polymorphisms (CNPs) were excluded from data analysis according to the CNP database generated in our laboratory and the Database of Genomic Variants (http://projects.tcag.ca/variation).

Zhang R., Kim Y.M., Wang X., Li Y., Lu X., Sternenberger A.R., Li S, & Lee J.Y. (2015). Genomic Copy Number Variations in the Myelodysplastic Syndrome and Acute Myeloid Leukemia Patients with del(5q) and/or -7/del(7q). International Journal of Medical Sciences, 12(9), 719-726.

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Transcriptome Analysis of Cell Lines and Samples

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Total RNA from the different cell lines, cervical scrapes, and biopsies was extracted with the NucleoSpin RNA Kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany) according to the manufacturer's instructions. RNA was quantified by absorbance at 260/280 nm. For microarray analysis, RNA quality was determined using an Agilent 2100 Bioanalyzer and the RNA 6000 NanoChip Kit (Agilent Technologies, Santa Clara, CA, USA). Double stranded complementary DNA (cDNA) was generated from 10µg of RNA using the cDNA Synthesis Kit System (Roche Applied Science) and purified with the GenEluteTM PCR Clean-Up Kit (Sigma-Aldrich Quimica, S. A. de R.L. de C.V.); thereafter, the cDNA was labeled with Cy3 and hybridized in a Human Gene Expression Array 12x135K (Roche Applied Science). Microarrays were scanned on the MS200 Scanner and the data obtained was processed using DEVA ver 1.2 software (Roche Applied Science). Fluorescence intensities were normalized using the RMA algorithm and the information was subsequently analyzed with CLC Main WorkBench ver. 7.0.3 software. Genes that were differentially expressed with a fold-change >1.5 and that exhibited a permutation p-value <0.05 were selected.

Alvarado-Ruiz L., Martinez-Silva M.G., Torres-Reyes L.A., Pina-Sanchez P., Ortiz-Lazareno P., Bravo-Cuellar A., Aguilar-Lemarroy A, & Jave-Suarez L.F. (2016). HOXA9 is Underexpressed in Cervical Cancer Cells and its Restoration Decreases Proliferation, Migration and Expression of Epithelial-to-Mesenchymal Transition Genes. Asian Pacific journal of cancer prevention : APJCP, 17(3).

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Transcriptomics of Streptococcus pneumoniae

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The high density Agilent expression arrays of S. pneumoniae were processed at the Functional Genomics Core Facility, Institut de Recerca Biomèdica, Barcelona, Spain. The arrays included one or two sets of 17 probes (average size of 60 nucleotides) for each 2037 protein coding genes from S. pneumoniae R6. Using 25 ng of total RNA as template, cDNAs were obtained from using the Trans-Plex WTA2 kit (Sigma). These cDNAs were labelled with Cy3 using the Agilent Genomic DNA ULS™ (Universal Linkage System) kit. A total of 250 ng of labelled cDNA were used for hybridization (40 h at 65°C) and scanning was performed with a Roche MS200 scanner. The raw data were extracted and normalized using the Agilent Feature extraction software v11.5.1.1. The median expression of every probeset was calculated and the result was scaled by log₂ and normalized according to quantile using the Bioconductor software (www.bioconductor.org/). A principal component analysis was then carried out using the Partek Genomics Suite 6.4. The significance of differential gene expression was determined using the ANOVA test. Each microarray experiment was carried out in duplicate using cDNA prepared from two independent cultures.

Ferrándiz M.J., Martín-Galiano A.J., Arnanz C., Camacho-Soguero I., Tirado-Vélez J.M, & de la Campa A.G. (2016). An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene. Nucleic Acids Research, 44(15), 7292-7303.

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