RNA-Seq of strain GDNA: aerobic acetate R1
The transcriptomes were extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research, Irvine, CA, USA), and were further purified using Turbo DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA) to eliminate DNA. rRNA was removed from the transcriptome samples using the Ribo-Zero rRNA Removal Kit (Epicentre Biotechnologies; Madison, WI, USA). The quality of the resulting RNA library was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and only the samples with an integrity value 8-10 were selected for transcriptomic analysis. First-strand cDNA was synthesized using the purified transcriptomes as the templates. Second-strand cDNA was synthesized in a reaction mixture containing Second-Strand Synthesis Kit (New England Biolabs; Ipswich, MA, USA). cDNA was purified using the Qiagen purification kit, followed by end repair using NEBNext End Repair Module (New England Biolabs). Antisense strand DNA was digested in the samples using the Uracil-Specific Excision Reagent Enzyme Kit (New England Biolabs), followed by a PCR to amplify the cDNA. The constructed sequencing libraries were sequenced as paired-end reads (with 150-200 bp read length) on the Illumina NovaSeq 6000 system (Illumina; San Diego, CA). Adaptor sequence-removing and sequence-trimming was achieved with Trimmomatic (Version 0.4).
A_CDM_1