ropanol and 0.07 vol. of 3 M sodium acetate, and then collected by centrifugation at 12,000 rpm for 35 min at 4uC. The RNA pellet was suspended in 10 ml of 70% ethanol, collected again by centrifugation, dried and suspended in formamide or nuclease free water. RNA purification and quantification-The RNeasy Mini Kit was used as per instructions of manufacturers to clean up RNA isolated by hot phenol method. Checked RNA concentration and quality by measuring 11179435 OD260 and OD260/280 of 1.5 ml sample using NanoDrop spectrophotometer. The first strand cDNA synthesis, second-strand cDNA synthesis, in-vitro transcription to synthesize amino-allyl modified aRNA and subsequently amino-allyl modified aRNA dye coupling was done using Ambion MessageAmpII Amino Allyl kit with Cy Dyes. The microarray slides were prehybridized in 56SSC, 0.1 mg/ml BSA and 0.1% SDS at 42uC for 1 h. Slides were washed 34 times in sterile fresh water at RT and dried by centrifugation at 200 g for 5 10 min in a 50 ml falcon tube layered with Kim wipe at its base as cushion. Prior to hybridization, <125 pico moles each of Cy5 and Cy3 labeled aRNA samples were combined and aRNA fragmented in 10 ml using RNA fragmentation Kit at 70uC for 15 min according to manufacture's instructions. The samples were placed on ice until ready to use or stored at 280uC. The fragmented aRNA was denatured at 65uC for 5 min. and hybridized to C.albicans microarray slide in GeneTAC hybridization station at 42uC for 1416 hrs. After the hybridization, the slides were washed in a dark staining tray as follows. Wash buffer 1:26 SSC, 0.2% SDS; Wash buffer 2:26 SSC; Wash buffer 3:0.26SSC. The slides were dried as described earlier. Scanning and quantification of the hybridized microarray slides were performed using the ScanArray Express software from Perkin Elmer. The microarray slide was scanned at 10 mm with fixed laser power and high and low PMT settings for both Cy5 and Cy3 channels. The ScanArray software was used for gridding and image quantification. The features such as those with artefacts like dust, streaks and odd morphology such as comets were flagged as bad spots. Low intensity and saturated spots were eliminated by flagging spots with spots with signal to noise ratio below 3.0. The Cy5 and Cy3 channels were normalized based on intensity dependent normalization in a plot of log vs log. Log2 ratio of the Cy5/Cy3 intensity for each spot was calculated. The data for triplicate spots for each gene in each array was merged and used for further statistical analysis. Significance analysis of microarrays was performed as described previously, with the exception of 1000 permutations to get differentially expressed genes with low false discovery rate. Heat map of the differentially expressed genes was 14530216 constructed using MeV v4.8.1 software. The experiment was repeated with freshly labelled RNA from Ki-8751 biological replicate and hybridized using the different dye for each biological replicate. GO Term Analysis GO term analysis was performed at CGD site for differentially upregulated genes with p- value,0.05, False Discovery Rate ,1% and ��Process��was chosen under ontology. The functional categories that are truly over-represented are shown in the table S3. Supporting Information 
Transcriptome analysis of hxk1 mutant Ai) Partial Heat map showing a comparative profile of HXK1 mediated few GlcNAc inducible genes. In the comparison between three microarray data sets viz. a) hxk1 mut vs. wild type in glucose b) GlcN
