CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts
- Equal contributors
1 Laboratory for Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
2 Bioinformatics Solutions Division, Nittetsu Hitachi Systems Engineering, Inc., Akashi-cho, Chuo-ku, Tokyo 104-6591, Japan
3 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, Hirosawa, Wako 351-0198, Japan
Genome Biology 2007, 8:R42 doi:10.1186/gb-2007-8-3-r42Published: 26 March 2007
Cap analysis gene expression (CAGE) technology has revealed numerous transcription start sites (TSSs) in mammals and has suggested complex promoter-based patterns of regulation. We developed the CAGE-TSSchip to detect promoter-based transcriptional activity. The CAGE-TSSchip is a customized oligonucleotide array that targets known TSSs identified by CAGE. A new labeling method, labeling capped transcripts from the 5'-end, had to be developed. The CAGE-TSSchip is accurate and sensitive, and represents the activity of each TSS.