A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples

Nucleic Acids Research

Volumn 35, Issue 21, 2007, Pages

  Leparc, Germán Gastón ^a,b   Mitra, Robi David ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; MESSENGER RNA; PRIMER DNA;

ACCURACY; ALTERNATIVE RNA SPLICING; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; EMBRYO; EXON; FALSE POSITIVE RESULT; FEMALE; FLANKING POLYMERASE CHAIN REACTION; GENE CASSETTE; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MALE; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; SEMI NESTED POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TISSUE MICROARRAY; VALIDATION STUDY; ANIMAL; METHODOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ALTERNATIVE SPLICING; ANIMALS; DNA PRIMERS; EXONS; HUMANS; MICE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 37549052484     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm989     Document Type: Article

References (16)

1. Stamm,S., Ben-Ari,S., Rafalska,I., Tang,Y., Zhang,Z., Toiber,D., Thanaraj,T.A. and Soreq,H. (2005) Function of alternative splicing. Gene, 344, 1-20.
2. Venables,J.P. (2004) Aberrant and alternative splicing in cancer. Cancer Res., 64, 7647-7654.
3. Johnson,J.M., Castle,J., Garrett-Engele,P., Kan,Z., Loerch,P.M., Armour,C.D., Santos,R., Schadt,E.E., Stoughton,R. et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141-2144.
4. Modrek,B. and Lee,C. (2002) A genomic view of alternative splicing. Nat. Genet., 30, 13-19.
5. Mockler,T.C., Chan,S., Sundaresan,A., Chen,H., Jacobsen,S.E. and Ecker,J.R. (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics, 85, 1-15.
6. Ohler,U., Shomron,N. and Burge,C.B. (2005) Recognition of unknown conserved alternatively spliced exons. PLoS Comput. Biol., 1 113-122.
7. Hiller,M., Huse,K., Platzer,M. and Backofen,R. (2005) Non-EST based prediction of exon skipping and intron retention events using Pfam, information. Nucleic Acids Res., 33, 5611-5621.
8. Sorek,R., Shemesh,R., Cohen,Y., Basechess,O., Ast,G. and Shamir,R. (2004) A non-EST-based method for exon-skipping prediction. Genome Res., 14, 1617-1623.
9. Florea,L. (2006) Bioinformatics of alternative splicing and its regulation. Brief Bioinform., 7, 55-69.
10. Sun,H. and Chasin,L.A. (2000) Multiple splicing defects in an intronic false exon. Mol. Cell Biol., 20, 6414-6425.
11. Stamm.S., Riethoven,J.J., Le Texier,V., Gopalakrishnan,C., Kumanduri,V., Tang,Y., Barbosa-Morais,N.L. and Thanaraj,T.A. (2006) ASD: A bioinformatics resource on alternative splicing. Nucleic Acids Res. 34, D46-D55.
12. Rozen,S. and Skaletsky,H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
13. Yeo,G.W., Van Nostrand,E., Holste,D., Poggio,T. and Burge,C.B. (2005) Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl Acad. Sci. USA, 102, 2850-2855.
14. Freitas,R.A. (1999) Appendix C: Catalog of Distinct Cell types in the Adult Human Body Landes Bioscience, Georgetown, TX.
15. Leparc,G.G. and Mitra,R.D. (2007) Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic Acids Res., 35, 3192-3202.
16. Malboeuf,C.M., Isaacs,S.J., Tran,N.H. and Kim,B. (2001) Thermal effects on reverse transcription: Improvement of accuracy and processivity in cDNA synthesis. Biotechniques, 30, 1074-1078.