Transcription profiling of E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells on a novel microarray design to validate the system

E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells were compared on a novel microarray design to validate the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 44,000 DNA features, and was designed to detect transcripts from all known genes, as well as about 5,000 potential genes, as identified by the NIA Mouse Gene Index 2.0. Seven external RNA controls were derived from intronic and intergenic yeast genome sequences, and 60-mer probes were spotted 10 time each on the slides. These spike-in RNA controls were diluted to cover 7 orders of magnitude in initial concentration, and used to define a function relating signal intensity to transcript abundance.本研究采用新型微阵列平台，对E12.5小鼠全胚胎、E12.5胎盘、胚胎干细胞（embryonic stem (ES) cells）以及滋养层干细胞（trophoblast stem (TS) cells）开展比较分析，以验证该系统的有效性。该原位合成的60聚体寡核苷酸微阵列平台包含约44000个DNA探针位点，其设计目标为检测由NIA小鼠基因索引2.0（NIA Mouse Gene Index 2.0）所鉴定的全部已知基因与约5000个潜在基因的转录本。7种外部RNA对照样本源自酵母基因组内含子及基因间区序列，每张芯片上的60聚体探针均重复点样10次。这些外源掺入（spike-in）RNA对照样本被稀释以覆盖7个数量级的初始浓度范围，用于构建信号强度与转录本丰度之间的关联函数。