NEW SensiChip Array Detection System

The QIAGEN SensiChip System (developed by QIAGEN and Zeptosens AG) uses innovative planar waveguide (PWG) technology to reduce background interference and dramatically increase the signal-to-noise ratio. This enables microarray analysis with as little as 1 µg total RNA — without amplification steps to give the true gene expression profile.

Features and benefits

• Complete microarray and detection platform
• Customized arrays with highly selective 70mer oligos
• DNA arrays with fluidic cells for high reproducibility and fast implementation
• Flexibility to scale up from low to high throughput
• High sensitivity to analyze expression patterns using 1 µg total RNA and perform multiple experiments with limited amounts of starting material

Principle

PWG technology provides highly sensitive detection with low background and high signal-to-noise ratios. A laser beam is directed into the thin PWG layer by a coupling grating. The light propagates within this PWG layer and generates a strong electromagnetic field (see figure "Planar Waveguide Principle"). This evanescent field decays exponentially in relation to the distance to the PWG layer, limiting its penetration depth to approximately 300 nm. Detection of fluorescent molecules is restricted to the sensing surface with the capture probes and their bound target molecules with no background noise beyond the penetration depth of the field.

Planar Waveguide Principle

Innovative PWG technology used by the SensiChip System provides excitation that is strictly confined to the surface. This results in high signal-to-noise ratios and improved sensitivity.

The SensiChip System provides high sensitivity without amplification steps, which can introduce bias. Low- and medium-abundance transcripts can be analyzed with as little as 1 µg total RNA (see figure "High Sensitivity with Low Amounts of RNA"). Real-time RT-PCR analysis using the QuantiTect Probe RT-PCR Kit confirms results obtained with the SensiChip System. This shows that the SensiChip results accurately represent the gene expression pattern in the cell.

Each SensiChip DNA Array carries its own fluidic cell, which functions as a hybridization chamber. SensiChip DNA Array Bars contain 6 separate arrays (see figure "High Correlation of SensiChip Data and Real-Time PCR Analysis"), pre-assembled under clean-room conditions and ready to use. This eliminates tedious and error-prone handling of cover slips and provides highly reproducible results.

Each bar is individually bar-coded for efficient handling and tracking. The SensiChip DNA Array Bar Carrier is designed in a microplate format (see figure "High Correlation of SensiChip Data and Real-Time PCR Analysis") for use with multichannel pipets, allowing automated handling.

Procedure

QIAGEN provides customized SensiChip DNA Arrays made to your specifications. Simply provide the GenBank accession numbers for the genes of interest. QIAGEN SensiChip Services will then design 70mer oligos and spot them onto a SensiChip DNA Array.

Hybridization is conveniently carried out on the SensiChip HybStation using the optimized buffers in the SensiChip Buffer Set. The microarrays are read on the SensiChip Reader, with SensiChip Control Software for image acquisition and control of the reader. SensiChip View Software is available for image analysis on the same system.

High Sensitivity with Low Amounts of RNA

SensiChip analysis was carried out using 96 mouse-brain specific capture probes (kindly provided by Lion Biosciences) spotted in duplicate. The target RNA was reverse transcribed and labeled using Cy5 and LabelStar reverse transcriptase, and the indicated amounts of RNA were used for hybridization. The number of spots with a signal-to-noise ratio (SNR) >3 is indicated below each microarray.

Applications

SensiChip technology provides high sensitivity for applications such as:

• Gene expression analysis of selected populations of cells
• Detection of low- and medium-abundance targets, such as kinases and transcription factors
• Analysis of limited amounts of starting material, such as cancer biopsies and FACS sorted cells
• Multiple experiments with limited amounts of starting material

High Correlation of SensiChip Data and Real-Time PCR Analysis

 A 

 B 

The low-abundance gene PBX2 was detectable by SensiChip analysis using as little as 500 ng total RNA. TaqManR real-time analysis with 10 ng total RNA confirms the abundance of transcription-factor genes TCF4 and PBX2.  A  Amplification plot using the QuantiTect Probe RT-PCR Kit.  B  Comparison of TaqMan threshold cycles and SensiChip SNR values.

Customized SensiChip DNA Arrays

 A  SensiChip Array Bar with SensiChip Arrays.

 B  SensiChip Array Bar Carrier with SensiChip Array Bars.