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.数据集文件：D02与对照组.csv 转录组测序（RNA-seq）：将分枝杆菌属菌株Mycolicicbacterium sp. ELW1的分批培养物接种于700 mL玻璃血清瓶中，以乙醚（diethyl ether, DEE）为唯一碳源，初始添加量为0.5 mmol（终浓度5 mM），于30℃、150 rpm摇床条件下培养。接种前，使用预先以果糖（1 mmol，终浓度10 mM）为碳源分批培养至对数生长后期的洗涤细胞，将初始接种光密度600 nm（OD600）调整至约0.35。同时留存部分果糖培养的细胞作为对照样品，用于后续转录组测序分析。经DEE培养约96小时后，通过离心（10,000相对离心力（RCF），离心5分钟，4℃）收集细胞，随后将每个转录组测序样品的细胞沉淀调整至约3.75×10^8个细胞。收集完成的细胞沉淀立即置于干冰乙醇浴中速冻4分钟，随后于-80℃保存待用。随后将细胞样品送至美国北卡罗来纳州立大学基因组科学实验室（北卡罗来纳州罗利市）进行RNA提取、核糖体RNA去除、Illumina（因美纳）RNA文库构建及测序。将定量后的文库按等摩尔浓度混合，随后使用Illumina NextSeq 2000 DNA测序仪（搭配P4 150 PE XLEAP流动槽及测序试剂套装，Illumina，美国）进行簇生成与测序。使用实时分析（Real Time Analysis, RTA）软件包生成原始碱基识别文件（bcl格式，即base call files），随后按样品将其解多路复用为FASTQ格式文件，用于数据提交。原始数据可在美国国家生物技术信息中心（NCBI）序列读取档案（Sequence Read Archive, SRA）中获取，对应生物项目编号为PRJNA1421072，生物样品编号为SAMN48782278，测序读取编号为SRR37182428至SRR371822433。 差异表达分析：使用CLC基因组学工作台v25.0（QIAGEN公司）完成差异表达分析。将测序读数比对至ELW1的染色体与质粒序列（登录号分别为CP193805.1与CP193804.1）。本分析以初始果糖培养的接种细胞为对照，将其余所有培养条件与孵育时间的样品与之比较，每组生物学重复数为：果糖培养接种组n=3，DEE培养组n=3。本次展示的文件即为ELW1在DEE培养与果糖培养条件下的完整差异表达分析结果。