Agilent Microarray Scanner

Detailed functioning/principle of the instrument:

Our group has designed custom Agilent microarrays for both Clostridium acetobutylicum and Clostridium botulinum to investigate global transcriptional changes under various scenarios. We have adopted a 4x44k format, i.e. one glass slide holds 4 separate microarrays, and each microarray has ~ 44,000 spots. We use Agilent hardware, reagents, and software in processing our microarrays and generally follow standard Agilent protocols.

Major components and their functions and part numbers:

Custom designed Agilent 4x44k microarrays

We have designed two 4x44k format microarrays for Clostridium acetobutylicum (one for transcriptional studies and one for ChIP-on-chip studies) and one 4x44k format microarray for Clostridium botulinum. The C. acetobutlicum ChIP-on-chip array differs from the other two only by the fact that the probes were designed only for the first half of the open reading frame. We use Agilent gasket slides (G2534-60012), Hi-RPM Gene Expression Hyb Kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=52806), and Gene Expression Wash Buffer Kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34851) for slide processing.

Agilent DNA Microarray Hybridization Chamber – SureHyb (http://www.chem.agilent.com/scripts/pds.asp?lPage=11373 )
The Agilent SureHyb Hybridization Chamber is used to hold the microarray, hybridization reagents, and labeled DNA samples together during hybridization.
Agilent DNA Microarray Hybridization Oven (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=18393 )
For hybridization, the Agilent Hybridization Oven is used at a temperature of 65°C and a rotation speed of 10 rpm. A rotisserie wheel provides the bubble-mixing action Agilent microarray slides require.
Agilent DNA Microarray Scanner (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=398 )
We use an Agilent DNA Microarray Scanner and the scan control software (version A.7.0.3) to scan all of our slides. Up to 48 slides can be added to the carousel at one time. We generally use Agilent’s Extended dynamic range to avoid spot intensity saturation.
Agilent Feature Extraction Software (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=2547 )

We use version 9.5.1 of the Feature Extraction Software to read and process our microarray data.

Note: For Further details contact Shawn Jones or Dinesh Indurthi .