Genome-wide mRNA profiling of PBMCs from TB patients (TB) and healthy controls (HC)

Transcriptome microarray analysis was conducted to examine the gene expression profiling of PBMCs from active TBs and HCs. All 18,853 mRNAs in the microarray were used to draw a Heatmap of differential genes according to their expression levels. The genes that exhibited significant changes in expression were used for further validation. The TB group (n=15) exhibited a significantly different profile compared to the HC (n=15) group (Fig. 1a). A total of 1,595 differentially expressed mRNAs were identified between the two groups. Of these, 335 mRNAs were up-regulated (fold change ≥ 2), and 1,260 mRNAs were down-regulated (fold change ≥ 2). RNA samples from each group were used to generate fluorescence labeled cRNA targets for the Agilent Whole Human Genome Oligo Microarray (4 × 44 K, including ~41,000 genes and transcripts). Labeled cRNA targets were then hybridized with the slides. After hybridization, slides were scanned on the Agilent Microarray Scanner (Agilent Technologies). Data were extracted with Feature Extraction software 10.7 (Agilent Technologies). Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6.1 (Agilent Technologies). The microarray experiments were performed by following the protocol of Agilent Technologies at Shanghai Biotechnology Corporation. A total of 1,595 differentially expressed mRNAs were identified between the two groups.