Lactobacillus rhamnosus Lcr35 native strain and formulations were grown overnight at 37°C in De Man Rogosa Sharpe (MRS) medium (BIORAD, Mitry Mory, France). 59(6):2075).
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using the RNA L kit (Macherey Nagel, Duren, Germany) and DNA was removed using DNase digestion with the RNase-Free Dnase kit (Ambion). 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.
Data processing
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
