Minimizing off-target signals in RNA fluorescent in situ hybridization

Nucleic Acids Research

Volumn 38, Issue 10, 2010, Pages

  Arvey, Aaron ^a,b   Hermann, Anita ^c   Hsia, Cheryl C ^c   Ie, Eugene ^b,d   Freund, Yoav ^b   McGinnis, William ^c  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d GOOGLE INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; EMBRYO; FLUORESCENCE ANALYSIS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION PROFILING; GENE NUMBER; GENE TARGETING; NONHUMAN; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA HYBRIDIZATION; RNA PROBE; RNA SEQUENCE; SIGNAL DETECTION; SIGNAL NOISE RATIO; ANIMAL; ANIMAL EMBRYO; CHEMISTRY; DROSOPHILA MELANOGASTER; GENETICS; METHODOLOGY; PRENATAL DEVELOPMENT;

ABD A PROTEIN, DROSOPHILA; ABD-A PROTEIN, DROSOPHILA; DROSOPHILA PROTEIN; MESSENGER RNA; NUCLEAR PROTEIN; SEX COMBS REDUCED PROTEIN, DROSOPHILA; TRANSCRIPTION FACTOR;

ANIMALS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EMBRYO, NONMAMMALIAN; IN SITU HYBRIDIZATION, FLUORESCENCE; NUCLEAR PROTEINS; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA PROBES; RNA, MESSENGER; TRANSCRIPTION FACTORS;

EID: 77954108033     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq042     Document Type: Article

References (24)

1. Kosman,D., Mizutani,C., Lemons,D., Cox,W., McGinnis,W. and Bier,E. (2004) Multiplex detection of RNA expression in Drosophila embryos. Science, 305, 846.
2. Gregorieff,A., Pinto,D., Begthel,H., Destrée,O., Kielman,M. and Clevers,H. (2005) Expression pattern of Wnt signaling components in the adult intestine. Gastroenterology, 129, 626-638.
3. Pezo,R., Gandhi,S., Shirley,L., Pestell,R., Augenlicht,L. and Singer,R. (2008) Single-cell transcription site activation predicts chemotherapy response in human colorectal tumors. Cancer Res., 68, 4977-4982.
4. Levsky,J. and Singer,R. (2003) Fluorescence in situ hybridization: past, present and future. J. Cell Sci., 116, 2833-2838.
5. Paré,A., Lemons,D., Kosman,D., Beaver,W., Freund,Y. and McGinnis,W. (2009) Counting Hox transcripts within single cells in fixed Drosophila embryos: evidence for transcriptional bursting. Curr. Biol., 19, 1-6.
6. Raj,A., van den Bogaard,P., Rifkin,S., van Oudenaarden,A. and Tyagi,S. (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods, 5, 877-879.
7. Femino,A.M., Fay,F.S., Fogarty,K. and Singer,R.H. (1998) Visualization of single RNA transcripts in situ. Science, 280, 585-590.
8. Femino,A., Fogarty,K., Lifshitz,L., Carrington,W. and Singer,R. (2003) Visualization of single molecules of mRNA in situ. Methods Enzymol., 361, 245-304.
9. He,Z., Wu,L., Li,X., Fields,M. and Zhou,J. (2005) Empirical establishment of oligonucleotide probe design criteria. App. Environ. Microbiol., 71, 3753-3760.
10. Kane,M.D., Jatkoe,T.A., Stumpf,C.R., Lu,J., Thomas,J.D. and Madore,S.J. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res., 28, 4552-4557.
11. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
12. Rigoutsos,I., Huynh,T., Miranda,K., Tsirigos,A., McHardy,A. and Platt,D. (2006) Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc. Natl Acad. Sci. USA, 103, 6605-6610.
13. Manber,U. and Myers,G. (1993) Suffix arrays: A new method for on-line string searches. SIAM J. Comput., 22, 935-948.
14. Langmead,B., Trapnell,C., Pop,M. and Salzberg,S. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
15. Burrows,M. and Wheeler,D. (1994), Technical Report 124. Digital Equipment Corporation.
16. Healy,J., Thomas,E., Schwartz,J. and Wigler,M. (2003) Annotating large genomes with exact word matches. Genome Res., 13, 2306-2315.
17. Navin,N., Grubor,V., Hicks,J., Leibu,E., Thomas,E., Troge,J., Riggs,M., Lundin,P., Maner,S., Sebat,J. et al. (2006) PROBER: oligonucleotide FISH probe design software. Bioinformatics, 22, 2437.
18. Tweedie,S., Ashburner,M., Falls,K., Leyland,P., McQuilton,P., Marygold,S., Millburn,G., Osumi-Sutherland,D., Schroeder,A., Seal,R. et al. (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res., 37, D555-D559.
19. Mahaffey,J. and Kaufman,T. (1987) Distribution of the Sex combs reduced gene products in Drosophila melanogaster. Genetics, 117, 51-60.
20. Sánchez-Herrero,E. (1991) Control of the expression of the bithorax complex genes abdominal-A and abdominal-B by cis-regulatory regions in Drosophila embryos. Development, 111, 437-449.
21. Angerer,L. and Angerer,R. (1981) Detection of poly A+ RNA in sea urchin eggs and embryos by quantitative in situ hybridization. Nucleic Acids Res., 9, 2819-2840.
22. Brahic,M. and Haase,A. (1978) Detection of viral sequences of low reiteration frequency by in situ hybridization. Proc. Natl Acad. Sci. USA, 75, 6125-6129.
23. Cox,K., DeLeon,D., Angerer,L. and Angerer,R. (1984) Detection of mRNAs in sea urchin embryos by in situ hybridization using asymmetric RNA probes. De.v Biol., 101, 485-502.
24. Lecuyer,E., Parthasarathy,N. and Krause,H. (2008) Fluorescent in situ hybridization protocols in Drosophila embryos and tissues. Methods Mol. Biol., 420, 289-302.