miRNA microarray experiments were run as described previously [27] (link). In brief, epoxy-coated Nexterion glass slides were spotted using the miRBase version 16.0 locked nucleic acid (LNA) probe set consisting of 2,367 probes against human, mouse and rat miRNAs in 8 replicates (Exiqon, Denmark). For hybridization 1000 ng total RNA extracts from two biological replicates of each sorted cell population were used. End-labeling of miRNAs with Cy3 was performed using the Exiqon Power Labeling Kit (Exiqon, Denmark) together with synthetic spike-in controls according to the instructions of the manufacturer. Slides were hybridized after an initial wash step with Cy3-labeled total RNA samples for 16 h at 56°C in a Tecan HS 400 hybridization station at high agitation speed (Tecan, Austria). After hybridization, automated washing, and slide drying, arrays were immediately scanned using the Roche Nimblegen MS200 scanner (Roche, Germany) at 10 µM resolution, 100% laser-power and auto-gain settings.
Nimblegen ms200 scanner
Manufactured by Roche
Sourced in Germany, United States
The NimbleGen MS200 is a high-performance microarray scanner designed for analyzing DNA and protein microarrays. It is capable of scanning a wide range of microarray formats and slide sizes, providing reliable and accurate data for various applications.
Automatically generated - may contain errors
Lab products found in correlation
Qiaquick purification kit, by Qiagen (3 mentions)
Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Spss version 17, by IBM (1 mentions)
Rneasy kit, by Roche (1 mentions)
Nimblescan v2, by Roche (1 mentions)
Hs 400 hybridization station, by Tecan (1 mentions)
Powersoil kit, by Qiagen (1 mentions)
Fluostar optima microplate reader, by BMG Labtech (1 mentions)
Low input quick amp wt labeling kit, by Agilent Technologies (1 mentions)
Mobio powersoil dna isolation kit, by Qiagen (1 mentions)
Fastdna spin kit for soil, by MP Biomedicals (1 mentions)
13 protocols using nimblegen ms200 scanner
1
miRNA Microarray Profiling of Sorted Cell Populations
2
Transcriptomic Analysis of O. oeni
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O. oeni cells were harvested by centrifugation, frozen in liquid nitrogen and kept at -80ºC until RNA extraction. Total RNA extractions were performed using the Roche RNeasy kit following the manufacturer's instructions (Mannheim, Germany). RNA concentrations were calculated by measuring absorbance at 260 nm using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific SL, Alcobendas, Spain). cDNA was subsequently prepared. Samples were hybridized to the arrays for 18 hours at 42ºC. After washing, the arrays were scanned in a Roche Nimblegen MS 200 scanner. Raw data files (Pair and XYS files) were obtained from images using Nimblescan v2.6 software (Roche Nimblegen). Normalized gene expression values were obtained with Nimblescan software using the robust multichip average (RMA) algorithm as described by Irizarry et al. (2003a; 2003b) . Data univariate (ANOVA) analyses of transcriptomic data were conducted using SPSS version 17.0 (SPSS Inc., Chicago, IL, USA). Variable means showing statistical significance were compared using Bonferroni post-test comparisons at a significance level of 0.05, after testing the homogeneity of variance assumption between the various groups. The results were submitted to GEO (Gene Expression Omnibus Database, NCBI) under accession number GSE62036.
3
Microarray Profiling of Cross-species miRNA
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Cross-species microRNA microarray experiments were run as described previously (Hernández Bort et al., 2012 (link)). In brief, epoxy-coated Nexterion glass slides were spotted using the miRBase version 16.0 locked nucleic acid (LNA) probe set consisting of 2367 probes against human, mouse and rat miRNAs in 8 replicates. For hybridization, 800 ng total RNA extracts from two biological replicates of each cell line from exponential growth phase were hybridized against a common reference pool RNA from all samples. End-labeling of miRNAs was performed using the Exiqon Power Labeling Kit (Exiqon, Denmark) together with synthetic spike-in controls according to the instructions by the manufacturer. Slides were hybridized over night at 56 °C in a Tecan HS 400 hybridization station, followed by automated washing and drying with nitrogen (Tecan, Austria). Immediately after drying, arrays were scanned using the Roche Nimblegen MS200 scanner (Roche, Germany) at 10 μM resolution and auto-gain settings.
4
Profiling of Citrullinated Peptides in RA
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The custom-made microarray was performed as previously described (7 (link)). In brief, 16 amino acid–long peptides that covered all arginine residues of 1610 extracellular matrix proteins and RA-related proteins were synthesized in situ (Roche NimbleGen). For TNC, there were a total of 217 peptides, including both native and citrullinated variants of each peptide synthesized. Samples tested for reactivity against TNC-derived peptides included synovial and plasma ACPA pools containing CCP-reactive antibodies from 26 and 38 RA patients, respectively (33 (link), 34 (link)) Paired synovial fluid and serum samples from 1 RA patient taken at 2 time points 10 years apart were also screened. ACPA pools were run at a concentration of 15 μg/mL, whereas synovial fluid and plasma or serum samples were diluted 1/100 and tested for citrulline reactivity using a NimbleGen MS200 Scanner (Roche NimbleGen). A peptide signal intensity variation (spot size) of 25 pixels was used as a basis for calculating the median fluorescence intensities. The cutoff for positive signals was defined as 5× the fluorescence intensity of the 98th percentile of values for a set of monoclonal antibodies without citrulline reactivity. These were included in the same experiment and were tested at the same time.
5
Metagenomic Analysis of Soil Microbiome
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Total DNA was extracted from 0.5 g of well-mixed soil using the PowerSoil kit (MoBio Laboratories) according to the manufacturer's instructions. DNA quality and quantity were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc.), and with PicoGreen ® using a FLUOstar ® Optima microplate reader (BMG Labtech), respectively. DNA hybridization was performed using GeoChip 5.0 according to Yang et al. (2013) (link). Briefly, DNA samples were labeled with Cy-5 fluorescent dye using a random priming method, and purified with the QIA quick purification kit (Qiagen). The DNA was dried in a SpeedVac (ThermoSavant) at 45°C for 45 min. GeoChip hybridization was carried out at 42°C for 16 hr on a MAUI ® hybridization station (BioMicro). After purification, GeoChips were scanned by a NimbleGen MS200 scanner (Roche) at 633 nm, using a laser power and photomultiplier tube gain of 100% and 75%, respectively.
6
Labeling and Hybridizing DNA Microarray
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DNA was labeled with Dye Cy-5 by a random priming method as previously described (Yang et al., 2017 (link)) and the labeled DNA was purified with QIA quick purification kits (Qiagen, Valencia, CA, United States). SpeedVac (ThermoSavant, Milford, MA, United States) was used to dry DNA at 45°C for 45 min. We hybridized DNA with GeoChip 4.0 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, United States) at 42°C for 16 h, as described previously (Yue et al., 2015 (link)). The slides were scanned using a NimbleGen MS200 scanner (Roche, Madison, WI, United States) at 633 nm using 100% laser power and 75% photomultiplier tube gain. Signal intensities were quantified by scanned images.
7
Multiplex Peptide Microarray for Viral Serology
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A total of 33 clinical samples (serum, n = 15 and TIB supernatant, n = 18) were incubated in three 12-plex peptide microarray chips embedded with 12-mer peptides from the following viral proteins (the UniProt ID is provided in parentheses): CMV pp65 (P06725), EBV EBNA1 (P03211), EBV EBNA3 (P12977), EBV LMP2 (P13285), and EBV BMLF1 (Q04360). The 12-mer peptides were selected to entirely cover each protein sequence with an 11-amino acid overlap. A total of 3067 peptides spanned the five viral proteins, with each peptide represented seven times (seven technical replicates) on the microarray chip. The antibodies used in the peptide microarrays for detecting IgG responses to peptides was Alexa Fluor® 647 AffiniPure Goat Anti-Human IgG, Fcγ Fragment Specific, reconstituted to 1 mg/ml (Jackson ImmunoResearch, West Grove, PA; cat# 109-605-098). After incubation, the microarrays were scanned with a NimbleGen MS200 scanner (Roche Applied Science, Penzberg, Germany) and signal was extracted with an internal Roche software called SlideViewer. The signal intensity of each spot was measured, following which a recognition data matrix was produced.
8
Human Tissue RNA Expression Analysis
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Total RNA (150 ng) from a panel of 12 human tissues (bladder, brain, breast, colon, heart, kidney, liver, lung, muscle, ovary, prostate, and skin, BioChain) was processed using a Low Input Quick Amp WT Labeling Kit (Agilent), and 600 ng labeled product was hybridized to slides using a NimbleGen Hybridization Kit (cat. no. 05 583 934 001), then hybridized for 16 h at 42 degrees. This was done by DTU Multi Assay Core facility at the Center for Biological sequence Analysis, Technical University of Denmark. Slides were scanned using a Roche NimbleGen MS 200 scanner and data extracted with NimbleScan v.2.6.
9
Soil Microbial Community Analysis via GeoChip
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In mid-September 2013, three soil cores of 5.0 cm in diameter from a depth of 0-50 cm were randomly collected in each mesocosm and then well mixed as a composite soil sample by soil depth (0-10 cm, 10-20 cm, 20-30 cm and 30-50 cm). The soil samples were kept on ice before transportation to the laboratory. Soil samples were then sieved using 2-mm mesh to remove the plant roots and stones and preserved at -80 °C before DNA extraction. Soil samples of 0-10 cm were used for GeoChip 5.0 experiments because the topsoil was significantly affected by WTL and N deposition. Soil DNA was extracted using the MoBio PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA) according to the manufacturer's instructions. The DNA was further purified by precipitation with ethanol and then dissolved in nuclease-free water. Approximately 0.6 μg of co g of community DNA was labeled with the fluorescent dye Cy-3 and hybridized with GeoChip 5.0 at 67 °C for 24 h in an Agilent hybridization oven. Then, GeoChip microarrays were scanned using a NimbleGen MS200 scanner (Roche, Madison, WI, USA). The detailed descriptions of DNA extraction, purification, labeling, hybridization to GeoChip 5.0, raw data processing and statistical analyses were reported in a previous study (Wang et al., 2014a) .
10
Microarray Analysis of Lysosomal Neuroaxonal Dystrophy
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