Robots for Printing Microarrays Jianping Zhou Robot 2003 Spring

What Microarrays  Microarray are high density arrays of biological molecule elements printed (attached) on a solid microscope slide using x-y-z stage robotic systems.  The media carry information through fluorescent intensity, or ratio of intensities, at a particular location on the array.  Originally developed by U. Maskos of E.M. Southern in 1992  Improved in January 1999 by M. Eisen and P. Brown of Departments of Genetics and Biochemistry and the Howard Hughes Medical Institute, Stanford University School of Medicine  More than 200 companies worldwide engaged in the Development and application of this technology.

GeneChip ® Probe Array

Why Microarrays Investigate the patterns and differences of biologic molecular structure in a single experiment Microarray analysis techniques make possible simultaneously analyze the expression levels of large numbers of genes and study the activity of whole genomes, rather than the activities of single, or a few, genes.

Microarray Feature Content Nucleic acid, Protein, Organic, Cell, Tissue Elements Rows denote genes, column denote experiment condition / profiles, Oligonucletide

Microarray Feature High-density 50 ~ 130 um >25um < 200 um 1.28cm ~10 7 oligonucleotides / cm 2

Microarray Feature substrates Glass, Nylon, other polymers poly-L-lysine or aminosilane coated glass dimethyl-sulfoxide

How Microarrays

cDNA-Microarray Process

Signal Intensity Measure Average Difference –Throw out high and low probes –Exclude any PM-MM more than 3 SDs from mean –Average the differences of PM-MM

Microarray Data Classification Prediction ALL or AML Gene Value D26528_at 193 D26561_cds1_at -70 D26561_cds2_at 144 D26579_at 318 D26598_at 1764 D26599_at 153 Model New sample Microarray chipsImages scanned by laser Raw Data Clinical Data Learning Alg. Training Data

GeneMachine Omni Grid Arrayer (Stanford University) Printing Pin Robot for Microarrays

Robot for Microarrays (cont.)

Robot System Providers Beecher Instruments BioRobotics Cartesian Technologies Engineering Services Genetic Microsystems Genetix Gene Machines Genomic Solutions Intelligent Automation Systems Packard <

Microarrayer from IAG (Brook Automation) Microarrayer HT Reconfigurable head for grid patterns Capable of over 20,000 spots/slide Speed: 32 features/sec with 32 pin printhead 48 features/sec with 48 pin printhead Large feature tips: micron feature size Small feature tips: micron feature size Microarrayer Four-axis Seiko robotic arm 12-tip print head 96- or 384-well microtiter plates onto as many as 100 silanized glass microscope slides. Average spot size of 130 µm Capability to adjust the spot-to- spot spacing Spot 19,200 elements (the contents of 200 microtiter plates) or more onto a single slide.

BioGrid from BioRobotics Density: print up to 83,000 samples per membrane. Print heads available for PCR product and bacterial clones. Compatible with 96 and 384 well microplates Friendly software - just fill in the boxes. Track your samples with automatic bar code reading. Requires only 60cm x 60cm of precious bench space. Macroarraying onto nylon membrane Speed: array 36,000 clones onto each of four 22cm membranes in just 1 hour.

BioChip Arrayer from PerkinElmer High precision plus accurate delivery µm spots at 250 µm spacing A precision X-Y-Z stage 4-PiezoTip transfer head 10 µm resolution in XY coordinates 50 µm resolution in Z coordinate Six predefined labware positions for microplates (96/384/1536) and glass slides

Microarrays Future  Microarrays contain live cells that express a cDNA of interest  Fluidic microarrays, a system for massively parallel signature sequencing (MPSS) randomly ordered microbeads can be analyzed simultaneously.  A new ‘scanometric’ detection system based on gold-nanoparticle-promoted silver reduction has been reported to be 100 times more sensitive than fluorescence system

Reference Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods Enzymol. 1999;303: Dietmar H Blohm* and Anthony Guiseppi-Elie, New developments in microarray technology. Current Opinion in Biotechnology 2001, 12:41-47 Priti Hegde, Rong Qi, Kristie Abernathy, Cheryl Gay, Sonia Dharap, Renee Gaspard, Julie Earle- Hughes, Erik Snesrud, Norman Lee, and John Quackenbush,A Concise Guide to cDNA Microarray Analysis, Biotechniques, 29(3), Sept 2000,