Total RNA was extracted and purified by using Trizol (Invitrogen, Carlsbad, CA, USA) and RNeasy cleanup kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer’s protocol. The total RNA yield was quantified by spectrophotometric analysis (NanoDrop Technology, Cambridge, UK) and the quality was verified by gel electrophoresis.
Label
cy3
Label protocol
Agilent oligonucleotide microarrays technology was used for monochromic analysis, in which probes (size: 60bp; three replicates for each ORF) from the two groups were labeled by incorporation of cyanine 3 (Cy3) (Agilent Technologies, Palo Alto, CA, USA).
Hybridization protocol
The purified Cy3-labeled cRNA was hybridized to Agilent 60-mer oligo-chips (Agilent Technologies, Palo Alto, CA, USA) in a rotary oven (0.011×g, 60°C, 17 h).
Scan protocol
Agilent scan G2565BA; Resolution:5μm.
Description
None
Data processing
Feature extraction software provided by Agilent (version 7.5, Agilent Technologies, Palo Alto, CA, USA) was used to quantify the intensity
of the fluorescent images and to normalize the results by subtracting local background fluorescence, according to the manufacturer’s instructions.
Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018
