Animals were sacrificed, ex-sanguinated and hearts were rapidly frozen in liquid nitrogen, and subsequently stored at -80oC. Infected tissues were taken from mice injected with 3x105 C.albicans blastospores into the tail vein. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TRIzol; Invitrogen). For cDNA labeling, either 20 mg of total RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42oC for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum.
Data processing
dye swap and intensity dependent (LOWESS) normalization
