Single molecule fluorescence microscopy for ultra-sensitive RNA expression profiling

Jan Hesse, Jaroslaw Jacak, Stefan Howorka, Leila Muresan, Fritz Aberger, Gerhard Schütz

Research output: Chapter in Book/Report/Conference proceedingsConference contributionpeer-review

1 Citation (Scopus)

Abstract

We developed a microarray analysis platform for ultra-sensitive RNA expression profiling of minute samples. It utilizes a novel scanning system for single molecule fluorescence detection on cm2 size samples in combination with specialized biochips, optimized for low autofluorescence and weak unspecific adsorption. 20 μg total RNA was extracted from 106 cells of a human keratinocyte cell line (HaCaT) and reversely transcribed in the presence of Alexa647-aha-dUTP. 1% of the resulting labeled cDNA was used for complex hybridization to a custom-made oligonucleotide microarray representing a set of 125 different genes. For low abundant genes, individual cDNA molecules hybridized to the microarray spots could be resolved. Single cDNA molecules hybridized to the chip surface appeared as diffraction limited features in the fluorescence images. The à trous wavelet method was utilized for localization and counting of the separated cDNA signals. Subsequently, the degree of labeling of the localized cDNA molecules was determined by brightness analysis for the different genes. Variations by factors up to 6 were found, which in conventional microarray analysis would result in a misrepresentation of the relative abundance of mRNAs.

Original languageEnglish
Title of host publicationUltrasensitive and Single-Molecule Detection Technologies II
DOIs
Publication statusPublished - 2007
EventUltrasensitive and Single-Molecule Detection Technologies II - San Jose, CA, United States
Duration: 20 Jan 200723 Jan 2007

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
Volume6444
ISSN (Print)1605-7422

Conference

ConferenceUltrasensitive and Single-Molecule Detection Technologies II
CountryUnited States
CitySan Jose, CA
Period20.01.200723.01.2007

Keywords

  • Expression profiling
  • Microarrays
  • Oligonucleotides
  • Single dye detection
  • Ultra-sensitive biochip readout

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