Microarray analysis of HSC gene expression.

(A) Microarray hybridization and spotfinding. Microarray slides described in Figure 1 were hybridized with cDNA probes prepared from cells. Each cDNA probe was labeled with Cy3 and Cy5 fluorophores separately. A combination of these cDNA probes was hybridized with microarrays A (3000 × 2) and B (2000 × 2). A typical hybridization result was shown using the Cy3-labeled cDNA probe from Rh^loLin^−/loSca-1⁺c-kit⁺and the Cy5-labeled probe from Rh^hiLin^−/loSca-1⁺c-kit⁺cells. (B) Statistical analysis and selection. A typical example showing the microarray hybridization results obtained from 2 experiments scanned by Genescanner (Molecular Dynamics) and analyzed by SpotUnite and SpotSelection programs (see text for details). (C) RT-PCR assays. To confirm the differential expression of genes between the Rh^lo and Rh^hi cells, 15% candidate genes were analyzed by RT-PCR as described in “Materials and methods.”