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

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). 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古菌嗜酸热原体（Thermoplasma acidophilum）开展全基因组基因表达水平变化的探究。相关分析详情详见Sun N、Pan C、Nickell S、Mann M、Baumeister W、Nagy I 撰写的《Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions》（已投稿）。本研究采用RNeasy Protect Bacteria试剂盒（Qiagen公司）分离嗜酸热原体的总RNA；转录组分析使用罗氏尼姆布基因（Roche NimbleGen）微阵列的TI273075型60mer芯片（冰岛尼姆布基因系统有限责任公司，NimbleGen Systems of Iceland, LLC）完成。针对全部1482条蛋白序列设计探针，并以Cy3进行标记，每条蛋白序列对应的探针中位数为20个，每个探针在芯片上重复5次且在芯片表面随机分布；未使用的芯片位点由GC含量匹配的随机生成探针填充。数据分析采用ArrayStar v2.0软件（DNASTAR公司）完成。需氧组与厌氧组各设置3次独立生物学重复。