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DNA Microarray for CGH & Gene Expression Analyzer

  DNA Micro Array Analyzer

Agilent Microarray Scanner comes equipped with Agilent SureScan technology delivering precision microarray scanning for optimum results. SureScan technology is the result of Agilent.s design and engineering excellence.known for industry firsts that include .optical switches and the enabling technology.


  • Low level detection resulting from optimized precision optics, broad dynamic range, minimal ‎spectral cross talk that allow users to detect weak features, achieve rapid, accurate and dependable results
  • Uniform images and enhanced sensitivity with dynamic autofocus to keep features in focus ‎while scanning to minimize the effects of gradients and aberrations associated with glass slides
  • Extended dynamic range, an industry-leading wide dynamic range of 105 for high sensitivity ‎scanning without saturation
  • Fast scanning by simultaneous two-color scanning at 5 and 10 micron resolution, in about 8 ‎minutes per slide for fast results
  • Integrated platform complete with PC, barcode reader and image analysis software with ‎feature information easily easily collected and seamlessly linked to statistical analysis and data ‎interpretation
  • Laser-saver feature enables programmability to turn on and off according to a given lab>s ‎workflow needs, thereby increasing the laser’s lifespan while reducing instrument maintenance
  • Automate extraction and analysis of Agilent microarrays with hands-free grid placement and a ‎barcode-enabled data tracking linked to microarray design and analysis protocols
  • Result confidence with Feature Extraction software that uses replicate, population, and spike-in ‎statistics to monitor array processing, report p-values, flag suspect data, and generate QC reports
  • Easily share information with standard format data output including tab-delimited text and ‎MAGE-ML that can be imported into a variety of microarray data analysis packages

Core elements include 1:1 PMT Adjustment capability, automatic Laser Power Control to eliminate laser drift and the industry-first Dynamic Autofocus feature that enhances scanning sensitivity and data reliability.

Agilent industry-first Dynamic Autofocus feature. This unique capability increases scanning sensitivity by continually focusing and re-focusing up to over 1 million times during the scanning process. This continual adjustment of the focal plane corrects for common glass abnormalities and gradients as well as any potential slide movement within the scanner.

The scanner is also optimized for high-signal-to-noise performance in the channels for cyanine 3 (550-610 nm) and cyanine 5 (650-750 nm), with a wide dynamic range and low crosstalk. This feature allows measurement of a very broad range of gene expression levels for higher data confidence at lower signal levels

Automatic Laser Power Control - Agilent designed its microarray scanner with a unique external laser ‎power modulation feature on its green SH-YAG (532 nm) and red HeNe (633 nm) lasers to continuously compensate for shortterm laser fluctuations. Agilent.s laser stability mechanism adjusts instantaneously for more reliable scanning data.

Complete, integrated scanning platform that offers you the capability of walkaway scanning for any mix of 1 x 3. microarrays combined with the power-packed feature extraction software

Automatic feature extraction of Agilent microarrays and linking to microarray design file information facilitates data analysis. Flexible background subtraction method based on multiple userselectable background techniques

Rosetta gene expression data analysis system users will appreciate the FTP function and capability to choose the data format for export (GEML or MAGE, JPEG or TIFF).

Agilent takes microarray scanning to new heights with its second generation platform that enables industry-standard 1» x 3» (25mm x 75mm) glass slide formats.

  • Completely or partially fill the 48-slide, load and go. carousel for scanning. Either way,
    You will save time.
  • Load your microarray slide, lock it into place in the secure
    slide holder and place in the carousel for convenient, walk-away scanning.
  • Agilent.s unique slide holder provides added protection against slide breakage. It accomodates
    Agilent 60-mer oligo microarray slides and most 1» x 3» glass slides from other sources
  • Agilent.s Microarray Scanner reads most industry standard barcode formats.

Application Software


CGH Analytics Software

Visually explore abberation patterns

The Agilent CGH Analytics 3.5 software provides an intuitive user interface for visually exploring, detecting and analyzing aberration patterns from multiple Comparative Genomic Hybridization (CGH) microarray profiles. It accepts data output from Agilent Feature Extraction software and displays chromosomal deletions and amplifications at multiple zoom levels simultaneously. Take advantage of the new joint analysis module to detect changes in both copy number and gene expression from experiments that have aCGH and gene expression data available

  • Visualization tools to explore single or multiple microarray profiles simultaneously at multiple ‎zoom levels for easy data comparison and pattern recognition
  • Multiple high speed statistical measures to assist detecting aberrant regions
  • Allows researchers to combine replicate probes within an array or to combine arrays with replicate samples
  • Joint CGH and gene expression analysis using t-tests and correlation analysis to detect associations between DNA copy number and gene expression profiles
  • Preloaded gene annotation information from the most recent genome builds
  • Convenient plug-in interface for data import and integration with custom third-party analysis ‎tools
  • Built-in step-by-step tutorial and help manual for first-time users
  • User-Friendly cytogenetic report that can be printed and shared with others.

Feature Extraction Software

Process microarray images with ease

  • Improved automatic gridding reduces manual gridding
  • Optional QC Chart Tool allows efficiently monitoring of microarray processing performance
  • QC Metric Sets with Thresholds provide guidance on identifying key metrics and establishing ‎normal ranges of metrics for Agilent Gene Expression two-color microarrays
  • Software updates – automatic notifications of new software releases
  • PDF QC Reports and QC Charts make sharing data convenient
  • Highly automated workflow reduces extraction time and effort
  • Optimized algorithms and protocols yield accurate data
  • Support for multiple scanner models provides microarray scanning flexibility
  • Application-specific QC reports provide metrics targeted to the experiment
  • Easy-to-use interface maximizes productivity

Comparative Genomic Hybridization (CGH) Applications

S.No. Item Description Part No. Reactions
1. Human Genome CGH Microarray Kit 244A
Each slide contains two identical 244K microarrays
● 236,000+ coding and noncoding human sequences represented
● 6.4 KB average probe spatial resolution
● Coverage spans both coding and noncoding regions, with emphasis on well-known genes, promoters, miRNAs, and telomeric regions.
G4411B 5 slides/kit
2. Human Genome CGH Microarray Kit 105A
Each slide contains two identical 105K microarrays
● 99,000+ coding and noncoding human sequences represented
● 15.0 KB average probe spatial resolution
● Coverage spans both coding and noncoding regions, with emphasis on well-known genes, promoters, miRNAs, and telomeric regions.
G4412A 5 slides/kit
3. Genomic DNA Labeling Kit PLUS
includes 7 reagents, including Cyanine 3- and 5-dUTP for labeling DNA targets for Agilent Oligo aCGH System.
5188-5309 50 labelings
4. Oligo aCGHLabeling Kit (for FFPE Samples) Contents includes labeling reagents, 10 purification columns and 10 collection tubes. 5190-0419 10 labelings
5. Genomic DNA Purification Module (for FFPE Samples) Contents includes 10 purification columns and 10 collection tubes 5190-0418 10 purifications
6. Oligo aCGH/ChIP-on-chip Hybridization Kit Contents includes hybridization buffer and blocking agent 5188-5220 25 hybridizations
7. Oligo aCGH Prehybridization Buffer (for TECAN HS) validated automated solution for hybrization and washing of aCGH 60-mer oligo microarrays 5190-0402 120 hybridization
8. Oligo aCGH/ChIP-on-chip Was Buffer Kit 5188-5226 40 washings

DNA Methylation Research

S.No. Item Description Part No. Reactions
9. Human CpG Island Microarray Kit, 105K 27,800 CpG islands covering 21 MB 237,220 probes in or within 95bp of CpG Islands Each slide contains one 244K microarray. G4492A 5 slides/kit
10. Human Promoter ChIP-on-chip Microarray Set, 244K
Set covers -5.5kb upstream to +2.5kb downstream of the transcriptional start sites Each slide contains one 244K microarray.
G4489A 2 slides/set
11. Stabilization and Drying Solution - 500 mL 5185-5979 25 hybridizations
12. Genomic DNA labeling Kit PLUS includes 7 reagents, including Cyanine 3-and 5-dUTP for labeling DNA targets for Agilent Oligo aCGH System 5188-5309 50 labelings
13. Oligo aCGH/ChIP-on-chip Hybridization Kit Contents includes hybridization buffer and blocking agent 5188-5220 25 hybridizations

Gene Expression Microarray Analysis

S.No. Item Description Part No. Reactions
14. Whole Human Microarray Kit, 4 x 44K 41,000+ unique human genes and transcripts 4 x 44K slide formats G4112F 5 slides/kit
15. Low RNA Input Fluorescent Linear Amplification Kit produces 0.25 - 2.0 μg of either cyanine-labeled cRNA (anti-sense) or cDNA (sense) from as little as 50 ng of total RNA, 5184-3523 20 reactions
16. Low RNA Input Linear Amplification Kit PLUS, Two-Color Low RNA Input Linear Amplification Kit Cynaine 3-CTP and Cyanine 5-CTP (1 vial each, 10 reactions/vial) 5188-5340 20 reactions
17. Gene Expression Hybridization Kit 5188-5242 10 hybridizations
18. Gene Expression Wash Buffer Kit 5188-5327 80 washings

miRNA Analysis

S.No. Item Description Part No. Reactions
19. Human miRNA Microarray Kit 470 human and 64 human viral miRNAs represented Slide contains eight identical 15K Microarrays G4470A 3 slides/kit
20. miRNA Labeling Reagent and Hybridization Kit include 3 reagents, including Cyanine 3-pCP for labeling and Hi- RPM Buffer 5190-0408 24 microarrays

Agilent 2100 bioanalyzer is the most successful microfluidics-based platform available ‎commercially, offering solutions for the analysis of DNA, RNA, proteins and cells


  • Faster than gels ( digital data in 30 minutes for quality and quantity of up to 12 samples)
  • Reproducible and complete digital data
  • Easy to use and share
  • Quantification of each individual fragment per sample offers purity results
  • 2-color analysis of fluorescently stained cells
  • Compliance Services allow work within regulated environments (e.g. QA/QC labs)
  • 2100 Expert software for easy digital handling and storage of all bioanalyzer data


2100 Expert Software

Agilent>s 2100 expert software is based on the flexibility of the integrated 2100 expert ‎platform. Since release B.02.03, the expert software supports the new Series II bioanalyzer assays and incorporates many new features designed to help you get even more from your digital data. It expands on the principles of providing expert assay knowledge embedded in the data analysis tools, allowing a more accurate automated and objective analysis by non-expert users

  • Data presented in electropherograms a nd gel-like images for electrophoresis assays as well as histogram and dotplot views for flow cytometry assays
  • Automatic and manual integration, as well as RNA fragment and smear analysis tools
  • Result flagging tool - rule definition for color-coded flag ging of pre-defined results
  • X-axis displayed on time, relative migration or size
  • Improved reporting, export and printing functions
  • Customizable result table and gel like-image
  • Integrated data comparison context, permits the comparison and overlay of results from different chips

Applications of 2100 Bioanalyzer

DNA analysis

Agilent’s Chip DNA assays allow you to automatically size and quantitate PCR fragments and restriction digests accurately and reproducibly. PCR and RT-PCR are among the most widely used techniques in molecular biology. While in some cases, it is sufficient to detect the presence or absence of a PCR product, in many cases quantitation of this product and detection of unspecific amplification is critical

  • Sizing accuracy - Normalization to two internal markers and a ladder.
  • Quantitation accuracy and reproducibility - Automated quantitation of each DNA fragment against internal standards.
  • High resolution of a large number of bands - Critical for any multiplex PCR application.
  • Broad linear dynamic range - Enables the detection of less abundant products, e.g. low abundance messages in multiplex RT-PCR amplifications or non-specific amplifications.
  • Sensitivity - LIF detection for fragments down to 0.1 ng.
  • Minimal sample consumption - Only 1 μL of material required per analysis

RNA Solutions

Due to the omnipresence of RNases, and the instability of RNA, integrity checks and sample ‎quantitation are essential steps before any RNA dependent application. Microfluidics ‎technology makes it easier and faster to analyze samples using just 1 µL of a RNA sample. ‎For mRNA samples the percentage of ribosomal impurities is calculated. RIN can be used as ‎a standard integrity measure that is independent of concentration, instrument or analyst.

  • Minimal sample consumption - use as little as 5 ng of total RNA or 200 pg of total RNA for analysis, saving most of your valuable preps!
  • Faster results - complete automated analysis 11 or 12 samples in about 30 minutes
  • Analyze Small RNA molecules, e.g. miRNA, siRNA, t-RNA within 6-150 nt range
  • RNase free - use RNase free reagents and chips to avoid sample degradation during analysis

Protein Solutions

Its fast and easy way to analyze a wide range of samples, each chip is capable of providing size, purity and concentration information for ten different protein samples. Simply add your samples, start the chip run, and watch the real-time data display. The lab-on-a-chip approach ‎eliminates handling SDS-PAGE slab gels, staining or imaging steps.

  • Fast results - Complete automated analysis of 10 samples in under 30 minutes
  • No manual staining and destaining steps required - All procedures automated during chip run
  • Analyze a large variety of protein samples - Cell lysates, column fractions, antibodies and purified proteins
  • Minimal sample consumption - Only 4 µl of protein sample required per analysis
  • Sizing and quantitation in one assay - Allows for relative and absolute quantitation
  • Alternative data display options - Results shown in gel-like image, electropherogram and tabular formats