DC3000 were grown in KB (King et al., 1954) to ~0.7x109 cfu/mL,The bacteria were centrifuged, washed twice with MM (Huynh et al., 1989), and resuspended in MM to 3x108 cfu/mL. The bacteria were cultured in MM for 6 h before being harvested for RNA extraction.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using a modified hot phenol procedure (Aiba et al. 1981), then purified by using RNeasy Midi kit following the manufacture instruction (Qiagen, Valencia, CA).
Label
biotin
Label protocol
According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.
Hybridization protocol
According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.
Scan protocol
According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.
Description
Gene expression data from DC3000 when grown in MM at 6hr(King et al., 1954).
Data processing
For each probe on the array, the median signal intensity was calculated using the NimbleGen extraction software. The data were normalized by using quantile normalization (Bolstad et al., 2003)available through the Bioconductor projec(http://www.bioconductor.org), and gene calls were generated by using the RMA algorithm (Robust Multichip Average) (Irizarry et al., 2003). The relative fluorescent intensities of each ORF were scaled by assuming a constant mean signal intensity of 1,000 signal units for each array.
