NimbleGen MS 200 Microarray Scanner

Unleash the full potential of NimbleGen microarrays

www.nimblegen.com

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Image Is Everything

Microarrays play an important role in genomics and life science research laboratories, providing highly sensitive and advanced tools for DNA analysis. Microarray-based experiments often involve considerable investment in time, resources, and valuable samples. A critical issue in the microarray research workflow is the ability to generate high-quality scanned images, which impacts both data quality and experimental results. Each laboratory requires a reliable, easy-to-use scanner that meets these requirements and can handle both current microarray design formats as well as the more complex, higher density arrays of the future.

Accelerate your microarray research using

The powerful features packed into the NimbleGen MS �00 Microarray Scanner are designed to meet your experimental demands with ease....

The MS �00 is the only scanner optimized to reveal the full potential and capture a comprehensive picture from high-density NimbleGen microarrays. The instrument combines advanced technology and design with a variety of convenient features to make your work easier:

• Slide magazine with a 48-slide autoloader• Integrated barcode reader• Onboard Integrated Laser Check slide• Built-in ozone mitigation system

All of these powerful features, plus many more, make the MS �00 the microarray scanner of choice for genomic research laboratories everywhere.

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Roche NimbleGen has built a reputation on delivering innovative, high-quality microarray solutions to life science and genomics researchers worldwide. This tradition continues with the NimbleGen MS �00 Microarray Scanner, built on state-of-the art technology enabling efficient microarray processing with high-resolution scanning and walk-away automation.

The MS �00 offers fast-scan capability with �-micron resolution of a high-density NimbleGen �.1M microarray in less than �0 minutes. The scanner’s high signal-to-noise ratio, high sensitivity, low limit of detection, and broad dynamic range improve data quality across a range of applications such as CGH/CNV, Gene Expression, ChIP-chip, and DNA Methylation.

High data quality: Advanced microarray technology when combined with sensitive, fast, high-resolution scanning provides a clear image of your data.

Fully automated: The 48-slide autoloader and integrated barcode reader allow for walk away operation.

Increased confidence in your data: Auto-PMT and autogain settings help provide consistent, reproducible experimental results.

Integrated system: High-density microarrays, optimized reagent kits, easy-to-use instrumentation, and seamless data analysis provide researchers with a unified workflow solution from Roche NimbleGen.

the NimbleGen MS 200 Microarray Scanner

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High-Resolution Images

The NimbleGen MS �00 Microarray Scanner offers a range of scanning resolutions from 40 micron down to � micron. For high-density NimbleGen �.1M microarrays, a �-μm resolution scan yields a better than five-fold increase in pixels per feature and consistently produces a higher quality image compared to a 5-μm resolution scan. The MS �00 is optimized to scan high-density NimbleGen arrays and generate array images without the need for additional image manipulation, such as cropping and reorientation, usually required by other scanners.

Faster Scans, Improved Sensitivity

The MS �00 generates scans quickly without sacrificing sensitivity or resolution. Two-color scanning at �-micron resolution of a NimbleGen �.1M microarray takes less than �0 minutes, increasing efficiency by allowing researchers to process more arrays at ultra-high resolution in less time.

Industry-leading low limits of detection, measured by minimal spectral and spatial crosstalk and full dynamic range, allow detection of low signals of up to �-5 times better than other comparable scanners, dramatically improving data sensitivity (Figure �).

The lower experimental noise values of high-resolution �-μm scans consistently produce high signal-to-noise ratio values in scans by the MS �00. High signal-to-noise ratios enable you to see a clearer picture of your data, get better quantification of your array images, and obtain more consistent, reliable data. Analysis results demonstrate a �0% improvement in signal-to-noise ratios for arrays scanned on the MS �00 compared to a competitor (Figure �).

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p Figure 3: High signal-to-noise ratio. Improved signal-to-noise is achieved with the MS 200. Using a test set of eight NimbleGen CGH Whole-Genome Tiling 3x720K arrays scanned at 2-µm resolution the signal-to-noise ratios (Chromosome X shift versus mad.1dr) were calculated and compared to values obtained from a competitor’s scanner.

p Figure 2: Significantly lower levels of signal detection. Detection sensitivity of the MS 200 was compared to competitor’s scanners using a slide containing titrations of known quantities of Cy3- and Cy5-labeled DNA and scanned at 2-micron resolution. The ability of each scanner to detect these titrations was measured.

p Figure 1: Images of a NimbleGen array. Comparison of a NimbleGen array scanned at 2- and 5-µm resolutions. The increased resolution at 2-µm scanning generates higher quality data and greater confidence in results obtained from high-density NimbleGen microarrays.

2-µm Resolution Scan 5-µm Resolution Scan

High-quality scans at your fingertips...the MS 200 Built for high-resolution,

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Walk-Away Automation

Built-in features combine to maintain high-quality, easily trackable samples for seamless experimental walk-away automation:

A 48-slide magazine reduces the risk of array degradation associated with surface contact, especially compared to instruments requiring individual slide holders.

An integrated barcode reader identifies and helps to ensure proper tracking of your samples.

Carbon-filtered airflow creates an ozone mitigation system helping to protect slides from signal degradation.

The MS �00 Data Collection software allows user-programmable settings for a single batch run that can handle multiple scans at different laser, filter, and PMT gain settings.

The software allows for easy setup and calibration, in addition to real-time visualization of the scanned image.

Performance Verification Tools

An onboard Integrated Laser Check (ILC) slide can be used to periodically verify scanner performance and provide results from tests done with 1� different calibration parameters. These results combined with the extensive Experimental Metrics report generated by our NimbleScan software provide quantifiable measurements to support the data from your microarray research experiments.

Minimal Footprint

The MS �00 requires only half the bench space of comparable scanners. With a compact 61 cm (�4 in) square footprint and a height of only 47 cm (18.5 in), the MS �00 easily fits on a standard laboratory bench.

high-performance and automated throughput

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Comparative Genome Hybridization (CGH)

Recent advances in high-resolution microarray technology have revealed genomic DNA copy number variation as a significant source of human genome variation, now thought to account for more nucleotide variation than single nucleotide polymorphisms (SNPs). With the emergence of high-resolution maps of common copy number variants (CNVs) in human populations, the impact of CNVs on human disease has become a key research focus.

The improved performance achieved with the NimbleGen Human CGH v�.0 arrays is further enhanced by scanning at �-μm resolution on the MS �00. This provides significant decrease in experimental noise, leading to more sensitive and reliable data (Figure 4).

Gene Expression

Gene expression profiles can provide key information to understanding diseases. The unique combination of long oligonucleotide probes and high probe density in NimbleGen Gene Expression microarrays enable easy, cost-effective analysis of eukaryotic and prokaryotic genomes.

The quality of data obtained after scanning NimbleGen Gene Expression 1�x1�5K arrays on the MS �00 was tested with the universal human reference and human brain reference RNA samples used in the Microarray Quality Control Consortium (MAQC) study. Highly precise profiles are evidenced by median CV values lower than 5% and interarray reproducibility of 0.99 (N=9). Data accuracy is supported by high concordance of the brain-to-universal fold-change values between NimbleGen microarray and TaqMan® data obtained from the MAQC report (Figure 5).

p Figure 4: Identification of a known insertion and deletion in a Burkett’s Lymphoma research sample. Arrows show locations of a known 35-Kb insertion and 382-Kb deletion in Chromosome 17. Lymphoma research samples were compared to reference DNA (normal human male) on a NimbleGen Human CGH 3x720K Whole-Genome v3.0 Array scanned using the MS 200.

p Figure 5: High-quality Gene Expression data using the NimbleGen MS 200 Microarray Scanner. Highly accurate gene expression profiles achieved with the NimbleGen Human Gene Expression 12x135K Array and MS 200 are evidenced by the high concordance with TaqMan® data (Nat. Biotechnol., 2006, 24:1151). Fold-change analysis of 961 genes in brain and universal reference RNA shows a correlation of 0.93 with a slope of 1.12.

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Human CGH 3x720K Whole-Genome v3.0 Array

Competitor’s 244K array

Segmental Duplications

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Chromatin Immunoprecipitation-on-chip (ChIP-chip)

ChIP-chip analysis reveals transcription factor DNA binding, chromatin structure, and DNase-I hypersensitivity and provides a means to discover novel genomic regulatory elements with high sensitivity, specificity, and reproducibility. For example, insulin strongly induces expression of Egr1, and therefore significantly more Egr1 DNA binding activity should be seen in insulin-treated cells compared to untreated cells (Figure 6). The sensitive, �-μm resolution scans of NimbleGen ChIP-chip arrays on the MS �00 readily discriminate differences in Egr1 promoter occupancy in insulin-treated and untreated samples.

DNA Methylation

NimbleGen DNA Methylation arrays enable sensitive, high-resolution, reproducible measurements of promoter and genic DNA methylation events, as well as allow differential methylation pattern analysis between cells, tissues, and tumor samples in research studies. These arrays, based on the latest genome builds, provide comprehensive coverage of whole genomes or significant regulatory elements at a considerable cost reduction per data point compared to other low density platforms.

Scans of DNA Methylation research samples analyzed on NimbleGen �.1M Deluxe Promoter arrays by the MS �00 and a competitor’s scanner were compared (Figure 7). The MS �00 plot shows slope and correlation values closer to 1 than that of the competitor, which demonstrates enhanced inter-array reproducibility when scans are performed on the MS �00.

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p Figure 6: NimbleGen ChIP-chip arrays and the MS 200 scanner reveal additional Egr1 DNA binding sites upon insulin treatment. ChIP-chip experiments using an Egr1 antibody on rat H4IIE cells samples treated with insulin were used to measure Egr1 promoter occupancy (blue boxes). These Egr1 ChIP samples were kindly provided by Dr. John Svaren, University of Wisconsin, Madison, WI, USA.

p Figure 7: High-resolution scans generate more reproducible DNA Methylation results. Two technical replicate slides within a 12-slide NimbleGen DNA Methylation array set were scanned at 2-µm resolution (MS 200) and at 5-µm resolution (competitor instrument). Scatter plots of Cy5/Cy3 ratios, slopes, and r2 values are shown.

MS 200 2-µm Scan

reproducible data across all applications

Competitor’s 5-µm Scan

NimbleGen Arrays Sample Preparation Hybridization Washing & Drying Scanning Data Analysis

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Bringing it all together: Roche NimbleGen workflow

Roche NimbleGen is committed to providing integrated solutions to help you get the most out of your microarray research experiments. We provide expertise and knowledge in convenient, user-friendly protocols that guide you through every integrated step of the workflow, and technical support whenever you need it.

Integration of the MS �00 into your NimbleGen microarray processing workflow significantly enhances data quality and reliability and provides an automated solution for scanning multiple arrays. The MS �00 Microarray Scanner is a key component of the NimbleGen workflow for processing microarrays from array design through data analysis.

NimbleGen Arrays Sample Preparation Hybridization Washing & Drying Scanning Data Analysis

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Optimized for NimbleGen arraysProprietary kits, instruments, and software are optimized to facilitate processing of NimbleGen microarrays from sample preparation to data analysis for a seamless microarray research solution.

Flexibility to manage your experimentsFrom catalog to custom designs, our arrays offer you the flexibility to design your experiment. In addition, our easy-to-use kits, accessories, and instruments accommodate high or low throughput to fully support the experiment you’ve designed.

Simplify your research with our integrated workflow Get the most out of your microarray workflow from an extensive line of NimbleGen products, all from an experienced single source supplier.

Wide variety of applications From chromosomal variation to gene expression and everything in between, see everything your array experiment reveals using NimbleGen arrays and the MS �00 Microarray Scanner.

solutions help ensure optimal research results

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Worldwide Support

Comprehensive installation and training is provided with the purchase of the MS �00 Microarray Scanner. Worldwide assistance is provided by Roche Microarray Technical Support. A 1�-month warranty is included with the scanner to cover all hardware and accessories provided with each installed system.

The MS �00 enables seamless data analysis with Roche NimbleGen’s NimbleScan and SignalMap software, as well as data compatibility with downstream, third-party analysis software.

Ordering InformationMicroarray Scanner Cat. No.

NimbleGen MS 200 Microarray Scanner 05 394 341 001

The following accessory can be ordered separately: Cat. No.

MS 200 Slide Magazine 05 471 478 001

Additional Workflow Accessories

Reagents Cat. No.

NimbleGen Dual-Color DNA Labeling Kit 05 223 555 001

NimbleGen One-Color DNA Labeling Kit 05 223 547 001

NimbleGen Hybridization Kit 05 583 683 001

NimbleGen Hybridization Kit, LS 05 583 934 001

NimbleGen Wash Buffer Kit 05 584 507 001

NimbleGen Array Processing Accessories 05 223 539 001

NimbleGen Sample Tracking Control Kit 05 634 270 001

Instruments Cat. No.

NimbleGen Hybridization System 4 (110V) 05 223 652 001

NimbleGen Hybridization System 12 (110V) 05 223 679 001

NimbleGen Hybridization System 4 (220V) 05 223 687 001

NimbleGen Hybridization System 12 (220V) 05 223 695 001

NimbleGen Microarray Dryer (110V) 05 223 636 001

NimbleGen Microarray Dryer (220V) 05 223 644 001

Order the complete microarray research solution

The NimbleGen MS 200 Microarray Scanner includes: • MS 200 Microarray Scanner• Slide magazine• Control unit• Data Collection software• NimbleScan software (3 licenses)• SignalMap software (3 licenses)• Operator’s Manual

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NimbleGen MS 200 Microarray Scanner SpecificationsPerformance

Limit of detection 0.17 fluorophores/µm2 ( 0.007 chromophores/µm2)

Dynamic range 105 (16-bit data format)

Pixel resolution 2 µm, 5 µm, 10 µm, 20 µm, 40 µm

Scan speed16/24 lines per second (8/12Hz); 2-color simultaneous data acquisition in 28 minutes for a 2.1M array at 2-µm resolution with autogain

Optical

Light sources Two solid-state lasers (532 nm and 635 nm)

Fluorescence detector(s) Two low dark current photomultiplier tubes

Gain adjustment 0.01-1000%

Optics High-aperture collection optics (NA 0.7)

Emission filters One predefined filter per laser

Autofocus Automatic, user-selectable slide types

Barcode reader Capable of reading NimbleGen, Code 39, and Code 128 barcode formats

Electrical

Power supply Auto sensing: 100 - 120V / 220 - 240V, 50/60 Hz

Power consumption 150VA

Approvals

EN 61010-1:2001, 61010-2-081/A1:2003, 60825-1/A1:2002,UL 61010-1:2004, IEC 61010-2-081/A1:2003, CAN/CSA-C22.2No. 61010-1:2004, CAN/CSA-C22.2 No. 61010-2-081:2004,CAN/CSA-E60825-1:2003

Physical

Slide magazine Holds up to 48 slides and allows automatic loading

Slide dimensions 1 in x 3 in (25 mm x 75 mm) glass slide

Outer dimensions Width: 60.0 cm (23.6 in), height: 46.6 cm (18.5 in), depth: 61.8 cm (24.4 in)

Weight Approximately 38 kg (84 lb)

Control Unit

Computer

HP dc7800 CMT with 3 GHz Intel Core 2 Duo processor8 GB Memory1.32 TB of total hard drive spaceCD/DVD-RW drive2 Ethernet RJ45 ports

Monitor 19 in LCD display with sound (1280 x 1024 resolution)

Operating system Microsoft Windows Vista Business (64-bit)

Published by:Roche NimbleGen, Inc.504 S. Rosa RdMadison, WI 53719 USA

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www.nimblegen.com/arraysupport

© 2009 Roche NimbleGen, Inc. All rights reserved.

For life science research only. Not for use in diagnostic procedures.

NIMBLEGEN and TAQMAN are trademarks of Roche. Other brands or product names are trademarks of their respective holders.