In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling

• Published in: Genome research 2003-05, Vol.13 (5), p.1011-1021
• Main Authors: Carter, Mark G, Hamatani, Toshio, Sharov, Alexei A, Carmack, Condie E, Qian, Yong, Aiba, Kazuhiro, Ko, Naomi T, Dudekula, Dawood B, Brzoska, Pius M, Hwang, S Stuart, Ko, Minoru S H
• Format: Article
• Language: English
• Subjects: Animals; Embryo, Mammalian - chemistry; Embryo, Mammalian - metabolism; Female; Gene Expression Profiling - methods; Gene Expression Profiling - statistics & numerical data; Gene Expression Regulation, Developmental - genetics; In Situ Hybridization - methods; In Situ Hybridization - statistics & numerical data; Mice; Mice, Inbred C57BL; Multigene Family - genetics; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - statistics & numerical data; Oligonucleotides - biosynthesis; Placenta - chemistry; Placenta - metabolism; Polymerase Chain Reaction - methods; Polymerase Chain Reaction - statistics & numerical data; Resources; RNA - genetics; Sensitivity and Specificity; Stem Cells - chemistry; Stem Cells - metabolism
• ISSN: 1088-9051; 1054-9803; 1549-5469
• DOI: 10.1101/gr.878903

Applications of microarray technologies to mouse embryology/genetics have been limited, due to the nonavailability of microarrays containing large numbers of embryonic genes and the gap between microgram quantities of RNA required by typical microarray methods and the miniscule amounts of tissue available to researchers. To overcome these problems, we have developed a microarray platform containing in situ-synthesized 60-mer oligonucleotide probes representing approximately 22,000 unique mouse transcripts, assembled primarily from sequences of stem cell and embryo cDNA libraries. We have optimized RNA labeling protocols and experimental designs to use as little as 2 ng total RNA reliably and reproducibly. At least 98% of the probes contained in the microarray correspond to clones in our publicly available collections, making cDNAs readily available for further experimentation on genes of interest. These characteristics, combined with the ability to profile very small samples, make this system a resource for stem cell and embryogenomics research.