ChIP-seq and In Vivo Transcriptome Analyses of the Aspergillus fumigatus SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence
Figure 2
RNA-seq and nCounter Analyses of ΔsrbA Confirms SrbA Regulation of ChIP-seq Target Genes in vitro and in vivo during Invasive Pulmonary Aspergillosis.
(A). Enrichment of RNA-seq differentially expressed genes in GO/Funcat categories of up- and down-regulated genes in srbA cells under hypoxia 120 minutes versus WT (B). Analysis of transcript levels of 12 of the ChiP-seq target genes in vivo in a murine model of invasive pulmonary aspergillosis for wild type (CEA10) and in vitro under normoxic/hypoxic conditions for ΔsrbA and wild type in vivo samples were at 48–96 hours post-infection (grey, n = 16). in vitro samples were wild type normoxia (red, n = 2) and hypoxia (blue, n = 6) followed by ΔsrbA under normoxia (red, n = 2) and hypoxia (blue, n = 6). Time under hypoxia for both wild type and ΔsrbA ranged from 30 to 120 minutes. Expression values are represented as total number of normalized counts per transcript. Quantitation and normalization was as follows: Digital counts for 60 genes (ChIP targets, housekeeping genes and other genes of interest) were adjusted for binding efficiency with background subtraction using the included positive and negative controls from the manufacturer as per NanoString nCounter data analysis guidelines. Data sets were normalized to facilitate across sample comparisons using the geometric mean of 20 stably expressed genes.