Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (WGA 2.1 Spike Test)

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. Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design 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.