Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. Thermoplasma acidophilum DSM 1728

Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted). Overall design: Total RNA of T. acidophilum was isolated with the RNeasy Protect Bacteria Kit (Qiagen). The transcriptomics analysis was performed on TI273075 60mer chips of Roche NimbleGen microarrays (NimbleGen Systems of Iceland, LLC). Probes were selected for all protein sequences (1482) and labelled with Cy3. The median number of probes per sequence is 20, and each probe is replicated 5 times on the chip. The probes are randomly distributed over the surface of the array. Unused features are filled with randomly generated probes of comparable GC content. ArrayStar v2.0 software (DNASTAR, Inc.) was used for the data analysis. Three independent biological replicates were processed for aerobic and anaerobic conditions, respectively.

本研究针对需氧与厌氧培养条件下的嗜酸热原体（Thermoplasma acidophilum）开展全基因组基因表达水平变化的探究，相关分析细节已详述于Na Sun、Cuiping Pan、Stephan Nickell、Matthias Mann、Wolfgang Baumeister及István Nagy的已投稿论文《古菌嗜酸热原体需氧与厌氧培养下的定量蛋白质组与转录组分析》。整体实验设计如下：采用RNeasy Protect细菌试剂盒（Qiagen）提取嗜酸热原体的总RNA；转录组分析使用罗氏尼姆布利根微阵列（Roche NimbleGen Microarrays，冰岛尼姆布利根系统有限责任公司）的TI273075型60mer芯片。针对全部1482条蛋白质序列设计探针，并以Cy3标记；每条序列对应的探针中位数数量为20，且每个探针在芯片上重复5次。探针随机分布于芯片阵列表面，未使用的位点由GC含量相近的随机生成探针填充。数据分析采用ArrayStar v2.0软件（DNASTAR有限公司）。需氧与厌氧培养条件各设置3次独立生物学重复。