Robots for Printing Microarrays

Jianping Zhou

91.548 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 FeatureContent

Nucleic acid, Protein, Organic, Cell, Tissue Elements

Rows denote genes, column denote experiment condition / profiles, Oligonucletide

Microarray FeatureHigh-density

50 ~ 130 um >25um

< 200 um

1.28cm

~107 oligonucleotides / cm2

Microarray Featuresubstrates

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

GeneMachine Omni Grid Arrayer (Stanford University)

Printing Pin

Robot for Microarrays

Robot for Microarrays (cont.)

Robot System Providers

•Beecher Instruments <http://www.beecherinstruments.com>•BioRobotics <http://www.BioRobotics.com/>•Cartesian Technologies <http://www.cartesiantech.com/>•Engineering Services <http://www.ESIT.com/>•Genetic Microsystems <http://www.geneticmicro.com>•Genetix <http://www.genetix.co.uk/>•Gene Machines <http://www.genemachines.com>•Genomic Solutions <http://www.genomicsolutions.com/>•Intelligent Automation Systems <http://www.ias.com>•Packard <http://www.packardinst.

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: 100-150 micron feature size Small feature tips: 75-100 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 - 180 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 FutureMicroarrays contain live cells that express a cDNA of interest

Fluidic microarrays, a system for massively parallel signature sequencing (MPSS). 107

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;303:179-205

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 2000,548-562