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Introduction to DNA Microarray Technology

Introduction to DNA Microarray Technology. Steen Knudsen, April 2005. DNA Microarrays consist of 100 - 1 million DNA probes attached to a surface of 1 cm by 1 cm (chip). By hybridisation, they can detect DNA or RNA:. If the hybridised DNA or RNA is labelled fluorescently it can

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Introduction to DNA Microarray Technology

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  1. Introduction to DNA Microarray Technology Steen Knudsen, April 2005

  2. DNA Microarrays consist of 100 - 1 million DNA probes attached to a surface of 1 cm by 1 cm (chip).By hybridisation, they can detect DNA or RNA: If the hybridised DNA or RNA is labelled fluorescently it can be quantified by scanning of the chip.

  3. DNA microarrays can be manufactured by: • Photolitography (Affymetrix, Febit, Nimblegen) • Inkjet (Agilent, Canon) • Robot spotting (many providers)

  4. Affymetrix photolitography • Each probe 25 bp long • 22-40 probes per gene • Perfect Match (PM) as well as MisMatch (MM) probes

  5. Febit/NimbleGen photolitography

  6. Robot Spotting

  7. InkJet (HP/Canon) technology

  8. Summary

  9. Image Analysis • Gridding: identify spots (automatic, semiautomatic, manual) • Segmentation: separate spots from background. Fixed circle (B), Adaptive circle C, Adaptive shape (D), Histogram • Intensity extraction: mean or median of pixels in spot • Background correction: local or global

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