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A link between multiple high throughput technology datasets

  • Bucher, Elmar
  • Kohonen, Pekka
  • Fey, Vidal
  • Mpindi, John
  • Sara, Henri
  • Pisto, Tommi
  • Edgren, Henrik
  • Kilpinen, Sami
  • Ojala, Kalle
  • Tiikkainen, Pekka
  • Vainio, Paula
  • Iljin, Kristiina
  • Sahlberg, Niko
  • Rantala, Juha K.
  • Mäkelä, Rami
  • Saviranta, Petri
  • Perälä, Merja
  • Nees, Matthias
  • Haapa-Paananen, Saija
  • Kallioniemi, Olli
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Our laboratory performs high-throughput screening (HTS) experiments using siRNA, miRNA and compound libraries on cancer-cell lines. We utilize three technologies: plate-based screens with different assays as endpoints, transfected cell arrays with up to four antibody endpoints, and protein lysate arrays allowing many immunostaining endpoints. In addition, we profile samples using at least three commercially available microarray technologies: gene expression using Affymetrix arrays, miRNA expression using Agilent arrays, and gene copy numbers (aCGH) using Agilent arrays. This enables us to study the same biological sample from multiple angles which provides a unique integrated opportunity to understand cancer. The database design presented here is based on the idea that different high-throughput technologies can be integrated at the gene level.

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