Catabolism of diethyl ether as a sole carbon and energy source by Mycolicibacterium sp. ELW1

File: D02 vs. control.csv RNA-seq: Batch cultures of strain Mycolicibacterium sp. ELW1 were grown in 700 mL glass serum bottles on diethyl ether (DEE) (0.5 mmol (5 mM final con.)) at 30C shaking at 150 rpm. The bottles were inoculated to an initial OD600 of ~0.35 from washed cells previously grown in batch culture on fructose (1 mmol (10 mM final con.)) to late log phase. Separate aliquots of the fructose-grown cells were saved for RNA-seq to serve as a control. After approximately 96 hr of growth on DEE, the cells were harvested by centrifugation (10,000 RCF; 5 min; 4℃) and then pelleted to approximately 3.75 x 108 cells per sample for RNA-seq. The cell pellets for RNA-seq were immediately frozen in a dry ice and ethanol bath for 4 min and then stored at -80℃ until used. Cell pellets were then submitted to the North Carolina State Genomic Sciences Laboratory (Raleigh, NC, USA) for RNA extraction, ribosomal depletion, and Illumina RNA library construction and sequencing. The final quantified libraries were pooled in equimolar amounts for clustering and sequencing on an Illumina NextSeq 2000 DNA sequencer, utilizing a P4 150 PE XLEAP flow cell and sequencing reagent kit (Illumina, USA). The software package Real Time Analysis (RTA), was used to generate raw bcl, or base call files, which were then de-multiplexed by sample into FASTQ files for data submission. Raw data can be found at NCBI's Sequence Read Archive (SRA) (Bioproject: PRJNA1421072, Biosample: SAMN48782278, Accessions: SRR37182428-SRR371822433). Differential expression analysis: We used CLC Genomics Workbench v25.0 (QIAGEN) to perform differential expression analysis. Reads were mapped to the ELW1 chromosome and plasmid (Accessions: CP193805.1 and CP193804.1). Differential expression analysis was performed using the initial fructose-grown inoculating cultures as the control to which all other growth conditions and incubation times were compared (sample sizes: fructose-grown inoculating culture, n = 3; DEE-grown, n = 3). The file displayed is the results of the full differential expression analysis comparing DEE-grown cells to fructose-grown cells of ELW1.