Pseudomonas fluorescens Pf0-2x (adnA-) was grown overnight in 50 mL of PMM.
Extracted molecule
total RNA
Extraction protocol
Samples were treated with the RNAprotect reagent (Qiagen Inc., Valencia, CA, USA) and the total RNA was extracted using the RNeasy Mini kit (Qiagen). RNA was treated with RQ1 RNase free DNase (Promega Corporation, Madison, WI, USA). RNA samples were quantified using a NanoDrop Spectrophotometer (Isogen Life Science, The Netherlands). The quality of the RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) at Tufts University Core Facility (Tufts University School of Medicine, Boston, MA, USA). First strand cDNA was synthesized from 10 mg total RNA with random hexamer primers from Invitrogen (Carlsbad, CA) using SuperScript Double-Stranded cDNA Synthesis kits (Invitrogen Corporation, Carlsbad, California, USA). The cDNA synthesis was carried out according to the NimbleGen protocol for synthesis of doublestranded cDNA.
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
This sample is of adnA mutant Pseudomonas fluorescens Pf0-2x. It is the second of two Pf0-2x biological replicates used in this experiment, each from separate cultures.
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.).
