This application requests funding for an Illumina Solexa high-throughput sequencing unit to strengthen and expand the existing the Biomedical Genomics Microarray Facility (BIOGEM) at the University of California, San Diego. BIOGEM is a campus core facility managed jointly by the School of Medicine and the Moores UCSD Cancer Center, an NCI-designated comprehensive cancer center. This application focuses on the need for a group of cancer biologists in the Center to pursue cutting-edge research in the post-genomic era. Taking advantage of the existing Solexa sequencer in a HHMI lab at UCSD, we have established several standard applications using the instrument for digital analysis of gene expression and genomic mapping of functional DNA elements. We are also developing other high-throughput sequencing-based technologies for mapping functional RNA elements, probing gene networks, and detecting gene and chromosomal rearrangements in cancers. Because of the limited access to the existing HHMI unit, we will house the Solexa in the BIOGEM facility, to allow applications of various digital technologies to specific cancer biology problems now under investigation in the laboratories of the prime users cited in the grant request.
This proposal seeks funding for the purchase of a Solexa instrument, the latest high- throughput sequencing system from Illumina. The instrument will be utilized by a group of UCSD cancer biologists to address an array of NIH-funded projects studying a variety of cancer-related problems, which are essential for development of strategies for cancer prevention and therapeutics.
|Xiao, Rui; Tang, Peng; Yang, Bo et al. (2012) Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. Mol Cell 45:656-68|
|Li, Hairi; Qiu, Jinsong; Fu, Xiang-Dong (2012) RASL-seq for massively parallel and quantitative analysis of gene expression. Curr Protoc Mol Biol Chapter 4:Unit 4.13.1-9|
|Fox-Walsh, Kristi; Davis-Turak, Jeremy; Zhou, Yu et al. (2011) A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation. Genomics 98:266-71|
|Yeo, Gene W; Coufal, Nicole G; Liang, Tiffany Y et al. (2009) An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 16:130-7|