substrain: CC72 genotype: Fusion of venus to the 3' end of rpoC in E. coli wild-type MG1655
Treatment protocol
When the OD600 of the cell culture reached 0.2, solid NaCl was added and dissolved to a final concentration of 0.5 M to induce osmotic stress. After 0.5 M NaCl treatment for 10 min, 20 min and 45 min, samples were collected, respectively.
Growth protocol
E. coli CC72 was grown in water bath to early-exponential phase (OD600 0.2) at 37°C in LB medium, then samples were collected.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.
Label
Cy3
Label protocol
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description
NC_000913.2+NC_000913.3 This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 20 min. It is the first of two biological replicates used in this experiment, each from separate cultures.
Data processing
Expression values were generated using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) based on the raw data (.pair file) and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).
Submission date
Feb 16, 2018
Last update date
Apr 12, 2018
Contact name
Zhe Sun
Organization name
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
