Batch fermentations were conducted in approximately 5 L of MTC medium with switchgrass as carbon source as described previously (Yang et al., 2008).
Extracted molecule
total RNA
Extraction protocol
RNA was isolated essentially described previously (Yang et al. 2010. PNAS. 107:10395–10400). 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 labeling, hybridization, and scanning following NimbleGen company's protocols.
Hybridization protocol
The labeling, hybridization, and scanning following NimbleGen company's protocols.
Scan protocol
The labeling, hybridization, and scanning following NimbleGen company's protocols.
Description
PU2_T2_R1
Data processing
Raw data: ORF/gene-level .calls files. Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm (Loess) 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).
