NimbleGen MS 200 Microarray Scanner

Unleash the full potential of NimbleGen microarrays

www.nimblegen.com

Accelerate your microarray research using

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. 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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the NimbleGen MS 200 Microarray Scanner

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 highresolution 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 scanners high signal-tonoise 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, easyto-use instrumentation, and seamless data analysis provide researchers with a unified workflow solution from Roche NimbleGen.

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

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 -m resolution scan yields a better than five-fold increase in pixels per feature and consistently produces a higher quality image compared to a 5-m resolution scan. The MS 00 is optimized to scan highdensity NimbleGen arrays and generate array images without the need for additional image manipulation, such as cropping and reorientation, usually required by other scanners.

2-m Resolution Scan

5-m Resolution Scan

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

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 ultrahigh 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 -m scans consistently produce high signal-to-noise ratio values in scans by the MS 00. High signal-tonoise 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 ).
Fluorophores/Sq. Micron Fluorophores/Sq. Micron

1 0.9 0.8 0.7 1 0.6 0.9 0.5 0.8 0.4 0.7 0.3 0.6 0.2 0.5 0.1 0.4 0 0.3
0.2 0.1 0.17

0.81

0.34 0.17
0.81

MS 200

Competitor 1

Competitor 2 0.34

p Figure 2: Significantly lower levels of signal detection. 0 Detection sensitivity of the MS 200 was compared to MS 200 Competitor 1 competitors scanners using a slide containingCompetitor 2 of titrations known quantities of Cy3- and Cy5-labeled DNA and scanned at 14 2-micron resolution. The ability of each scanner to detect these 12 titrations was measured.
ChrX/mad.1dr ChrX/mad.1dr 10 14 8 12 6 10 4 8 2 6 0 4
2 0 MS 200 Competitor 1 11.76 8.98

11.76 8.98

MS 200

Competitor 1

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

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high-performance and automated throughput

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 userprogrammable 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.

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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 -m resolution on the MS 00. This provides significant decrease in experimental noise, leading to more sensitive and reliable data (Figure 4).

Human CGH 3x720K Whole-Genome v3.0 Array

0.800 0.000 -0.800

35 Kb

0.800 0.000 -0.800

Competitors 244K array

382 Kb

10.000 6.000 3.000 0.000

Normal CNVs

5.000 0.000 -5.000

Segmental Duplications

5.000 0.000 -5.000

Known Genes

Figure 4: Identification of a known insertion and deletion in a Burketts 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.

Gene Expression
TaqMan Brain/Universal (log2)

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 1x15K 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).

r = 0.93 slope = 1.12

NimbleGen 12x135K Array Brain/Universal (log2)

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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Comparative Genome Hybridization (CGH)

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reproducible data across all applications

Chromosome 17

Insulin-Treated Cells

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, -m resolution scans of NimbleGen ChIP-chip arrays on the MS 00 readily discriminate differences in Egr1 promoter occupancy in insulin-treated and untreated samples.

Chromosome 8

Ratio Values

Ratio Values

Peaks

Peaks

Chromosome 17

Untreated Cells

Chromosome 8

Ratio Values

Ratio Values

Peaks

Peaks

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.
MS 200 2-m Scan

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 competitors 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.

Competitors 5-m Scan

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-m resolution (MS 200) and at 5-m resolution (competitor instrument). Scatter plots of Cy5/Cy3 ratios, slopes, and r2 values are shown.

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Bringing it all together: Roche NimbleGen workflow

NimbleGen Arrays

Sample Preparation

Hybridization

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.

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solutions help ensure optimal research results

Washing & Drying

Scanning

Data Analysis

Optimized for NimbleGen arrays Proprietary 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 experiments From 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 youve 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.

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Order the complete microarray research solution

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 NimbleGens NimbleScan and SignalMap software, as well as data compatibility with downstream, third-party analysis software.

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) Operators Manual

Ordering Information
Microarray Scanner
NimbleGen MS 200 Microarray Scanner
The following accessory can be ordered separately:

Cat. No. 05 394 341 001 Cat. No. 05 471 478 001

MS 200 Slide Magazine

Additional Workflow Accessories

Reagents
NimbleGen Dual-Color DNA Labeling Kit NimbleGen One-Color DNA Labeling Kit NimbleGen Hybridization Kit NimbleGen Hybridization Kit, LS NimbleGen Wash Buffer Kit NimbleGen Array Processing Accessories NimbleGen Sample Tracking Control Kit Cat. No. 05 223 555 001 05 223 547 001 05 583 683 001 05 583 934 001 05 584 507 001 05 223 539 001 05 634 270 001 Cat. No. 05 223 652 001 05 223 679 001 05 223 687 001 05 223 695 001 05 223 636 001 05 223 644 001

Instruments
NimbleGen Hybridization System 4 (110V) NimbleGen Hybridization System 12 (110V) NimbleGen Hybridization System 4 (220V) NimbleGen Hybridization System 12 (220V) NimbleGen Microarray Dryer (110V) NimbleGen Microarray Dryer (220V)

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NimbleGen MS 200 Microarray Scanner Specifications

Performance
Limit of detection Dynamic range Pixel resolution Scan speed Optical Light sources Fluorescence detector(s) Gain adjustment Optics Emission filters Autofocus Barcode reader Electrical Power supply Power consumption Approvals Physical Slide magazine Slide dimensions Outer dimensions Weight Control Unit HP dc7800 CMT with 3 GHz Intel Core 2 Duo processor 8 GB Memory 1.32 TB of total hard drive space CD/DVD-RW drive 2 Ethernet RJ45 ports 19 in LCD display with sound (1280 x 1024 resolution) Microsoft Windows Vista Business (64-bit) Holds up to 48 slides and allows automatic loading 1 in x 3 in (25 mm x 75 mm) glass slide Width: 60.0 cm (23.6 in), height: 46.6 cm (18.5 in), depth: 61.8 cm (24.4 in) Approximately 38 kg (84 lb) Auto sensing: 100 - 120V / 220 - 240V, 50/60 Hz 150VA 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-C22.2 No. 61010-1:2004, CAN/CSA-C22.2 No. 61010-2-081:2004, CAN/CSA-E60825-1:2003 Two solid-state lasers (532 nm and 635 nm) Two low dark current photomultiplier tubes 0.01-1000% High-aperture collection optics (NA 0.7) One predefined filter per laser Automatic, user-selectable slide types Capable of reading NimbleGen, Code 39, and Code 128 barcode formats 0.17 fluorophores/m2 ( 0.007 chromophores/m2) 105 (16-bit data format) 2 m, 5 m, 10 m, 20 m, 40 m 16/24 lines per second (8/12Hz); 2-color simultaneous data acquisition in 28 minutes for a 2.1M array at 2-m resolution with autogain

Computer

Monitor Operating system

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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.

05508517001 u 12/09

Published by: Roche NimbleGen, Inc. 504 S. Rosa Rd Madison, WI 53719 USA
www.nimblegen.com/arraysupport

2009 Roche NimbleGen, Inc. All rights reserved.