title: AresLabUCSC_Mouse_24K_MuSpliceV1
status: Public on Dec 29 2007
contact.city: Los Angeles
contact.first: Douglas
contact.last: Black
contact.state: CA
contact.address: 675 Charles E Young Dr S
contact.department: MIMG
contact.country: USA
contact.institute: UCLA
organism: Mus musculus
manufacture_protocol: Oligonucleotide and microarray design have been described previously (Clark et al., 2002; Srinivasan et al., 2005). To chose exons whose regulation was likely to be functionally significant, we used exons from 5 datasets: (i) Exons identified from the literature that exhibit neuron-specific or muscle-specific regulation, or have partially characterized mechanisms of regulation; (ii) Exons derived from genes coding for known splicing factors or protein kinases involved in splicing where EST, phylogenetic, and other evidence supports a role for these exons in regulating protein expression by coupling to NMD (similar to PTB exon 11); (iii) Exons in genes associated with cancer and tumor development, whose splicing is thought to have important functional effects on the encoded proteins; (iv) Exons derived from the MAASE database of alternative splicing (Zheng et al., 2005). These exons affect proteins that have well described functions in the Swiss-prot database; (v) a subset of the exons identified by Sugnet (Sugnet et al., 2004) as showing conserved regulation between human and mouse. The exon sets were combined, filtered for redundancies and used to build models for the corresponding transcripts. Oligonucleotide probes for the exon-exon junctions from skipped and included isoforms were designed, along with probes for sequence within the alternative exon itself and within adjacent constitutive exons.
  Oligonucleotides were spotted in duplicate. Briefly, 5' amino-linker containing oligonucleotides at 33uM in print buffer (150 mM NaPO4, 6.25% Na2SO4, 0.0005% SDS) were printed and covalently attached to Codelink slides (GE). Printing was done on a linear servo-driven robotic contact pin printer essentially as described by the DeRisi lab at UCSF (http://derisilab.ucsf.edu/arraymaker.shtml). Coupling and post-processing of slides were described previously (Clark et al., 2002).
  Clark, T. A., Sugnet, C. W., and Ares, M., Jr. (2002). Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907-910.
  Srinivasan, K., Shiue, L., Hayes, J. D., Centers, R., Fitzwater, S., Loewen, R., Edmondson, L. R., Bryant, J., Smith, M., Rommelfanger, C., et al. (2005). Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods 37, 345-359.
  Sugnet, C. W., Kent, W. J., Ares, M., Jr., and Haussler, D. (2004). Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput, 66-77.
  Zheng, C. L., Kwon, Y. S., Li, H. R., Zhang, K., Coutinho-Mansfield, G., Yang, C., Nair, T. M., Gribskov, M., and Fu, X. D. (2005). MAASE: an alternative splicing database designed for supporting splicing microarray applications. Rna 11, 1767-1776.