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Journal of Nucleic Acids
Volume 2012 (2012), Article ID 283560, 10 pages
Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray
1Section for Genomics and RNomics, Biocenter, Innsbruck Medical University, Fritz Pregl Strasse 3, 6020 Innsbruck, Austria
2Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
3Université de Lorraine, CNRS-UMR 7214 AREMS, 9 avenue de la Forêt de Haye, F-54506 Vandoeuvre-lès-Nancy, France
Received 30 November 2011; Revised 6 March 2012; Accepted 6 March 2012
Academic Editor: Ashis K. Basu
Copyright © 2012 Konstantinia Skreka et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Supplementary Figure 1: Self-self hybridization at 56°C of 5 μg (per dye) of labeled total mouse brain RNA. Diagrams of average intensity values show filtered results in logarithmic scale. The y axis represents values of AlexaFluor3 dye measurement at 532 nm and the x axis represents values of AlexaFluor5 dye measurement at 635 nm. Red spots represent all signals from LNA and DNA probes spotted on the microarray slide. Detection of 7SK RNA from antisense probes (a) without any modifications to the RNA labeling protocol, or (b) with the modified labeling protocol (see results). (c) Detection of tRNAs with the modified labeling protocol (see results).
Supplementary Table 1: Sequences of the ncRNA corresponding DNA probes spotted on the microarray. Nucleotide mismatches are shown in bold and positions with deletions are underlined. Hybridization position of the probe on the ncRNA is indicated with numbers at the end of the probes name. Abbreviations: MM1: one nucleotide mismatch; MM2: two nucleotides mismatches; D1: one nucleotide deletion; D2: two nucleotides deletions; RC: sense probe.
Supplementary Table 2: Filtered results corresponding to Figure 6. Fold changes are indicated as log2 values. Only ncRNAs differentially expressed above 2 folds are mentioned.