Batch fermentations were conducted in approximately 4 L of MM medium in 7.5-L BioFlo110 bioreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH, temperature and DOT probes and controls as described previously (Yang et al., 2008).
Extracted molecule
total RNA
Extraction protocol
RNA was isolated essentially described previously [26]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).
Label
Cy3
Label protocol
The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.
Hybridization protocol
The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.
Scan protocol
The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.
Description
AcR_F6_148h
Data processing
Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).
