Transcriptional Profile of C. diphtheriae

Custom microarrays (8 microarrays per slide) based on the published C. diphtheriae NCTC 13129 genome [39 (link)] were designed using Agilent’s eArray platform. The Agilent One-Color Microarray-Based Exon Analysis, Version 2.0 protocol was followed as per manufacturer directions. The random oligo primer mix was used for cDNA synthesis and Cyanine 3-CTP was used for subsequent cRNA synthesis. Total RNA collected from 3 independent biological replicates of each strain and condition was used for the synthesis of cRNA. Each sample was processed and run in individual wells. Arrays were washed as directed and scanned using an Agilent G2505C Microarray Scanner. For each well, the median of the gProcessedSignal for each gene probe was normalized by the mean of the entire sample set. Normalized values were log2 transformed and subjected to the J5 test using the CBER High-Performance Integrated Virtual Environment (HIVE) [40 (link)]. Genes with a log2 fold change greater than 1 and a J5 test value greater than 2 were considered significantly regulated. The microarray data and design are available at the Gene Expression Omnibus database (Accession: GSE131485).