Gene expression of FA19 MpeR mutant JF5 mid-log replicates were compared to previously deposited WT FA19 mid-log samples (GSM318543, GSM318544, and GSM318545)
Growth protocol
Isolates were grown to mid-log and late-log phase in GC broth @ 37°C with supplements and sodium bicarbonate: Shafer, W.M., L. F. Guymon, I. Lind, and P. F. Sparling. 1984. Identification of an envelope mutation (env-10) resulting in increased antibiotic susceptibilit
Extracted molecule
total RNA
Extraction protocol
RNA was isolated by a hot phenol method according to: Ducey, T. F., M. B. Carson, J. Orvis, A. P. Stintzi, and D. W. Dyer. 2005. Identification of the iron-responsive genes of Neisseria gonorrhoeae in microarray analysis in defined medium. J. Bacteriol.
Label
Biotin
Label protocol
Biotinylated cRNA was prepared according to Affymetrix Genechip® Expression Analysis Technical Manual prokaryotic protocol from 10ug of total RNA
Hybridization protocol
Arrays were hybridized using streptavidin phycoerythrin according to Affymetrix protocol ProkGE-WS2v3_450
Scan protocol
Arrays were scanned using Affymetrix GeneChip Scanner 3000
Description
JF5_2 mid-log.CEL
Data processing
Data was processed using Genechip Operating Software (GCOS) version 1.4 (Affymetix, Inc.) GCOS data was then imported into GeneSpring GX 7.3.1 (Agilent Technologies) Normalization was done per chip by dividing each measurement by the 50th percentile of all the measurements in that sample and per gene by dividing each gene by the median of its measurements across all samples. The cross-gene error model was operating based on replicates. The normalized data from all samples were filtered on genes flagged as present or marginal with the resulting gene list used for further gene expression analysis and clustering
