Microarray Methods in Drosophila Neurobiology

Overview

Journal Invert Neurosci

Date 2005 Sep 24

PMID 16180035

Citations 1

Authors

Christopher J Mee

Affiliations

Soon will be listed here.

Abstract

In the relatively short period since their development, DNA microarrays have been used increasingly in the study of genetic and cellular processes, thereby offering a genome-wide approach to gene expression studies. With the advent of genome sequencing programs for organisms from yeast to man, the number of organisms which now have ready-made commercial arrays continues to increase. Here, the principle of DNA microarrays is introduced, with particular attention being given to the role of this technology in studies of the nervous system of the fruitfly Drosophila melanogaster. The importance of experimental design and sample preparation, in line with minimum information about microarray experiment (MIAME) compliance, is emphasised. The technical platforms available to the Drosophila neurobiologist have been illustrated and a brief number of data analysis tools that are readily available reviewed.

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References

Brand A, Perrimon N . Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development. 1993; 118(2):401-15. DOI: 10.1242/dev.118.2.401. View

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C . Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; 29(4):365-71. DOI: 10.1038/ng1201-365. View

Wick I, Hardiman G . Biochip platforms as functional genomics tools for drug discovery. Curr Opin Drug Discov Devel. 2005; 8(3):347-54. View

Leemans R, Egger B, Loop T, Kammermeier L, He H, Hartmann B . Quantitative transcript imaging in normal and heat-shocked Drosophila embryos by using high-density oligonucleotide arrays. Proc Natl Acad Sci U S A. 2000; 97(22):12138-43. PMC: 17307. DOI: 10.1073/pnas.210066997. View

Hardiman G . Microarray platforms--comparisons and contrasts. Pharmacogenomics. 2004; 5(5):487-502. DOI: 10.1517/14622416.5.5.487. View

Fodor S, Read J, Pirrung M, Stryer L, Lu A, Solas D . Light-directed, spatially addressable parallel chemical synthesis. Science. 1991; 251(4995):767-73. DOI: 10.1126/science.1990438. View

Peng X, Wood C, Blalock E, Chen K, Landfield P, Stromberg A . Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics. 2003; 4:26. PMC: 166151. DOI: 10.1186/1471-2105-4-26. View

Kendziorski C, Zhang Y, Lan H, Attie A . The efficiency of pooling mRNA in microarray experiments. Biostatistics. 2003; 4(3):465-77. DOI: 10.1093/biostatistics/4.3.465. View

Cho R, Mindrinos M, Richards D, Sapolsky R, Anderson M, Drenkard E . Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet. 1999; 23(2):203-7. DOI: 10.1038/13833. View

10.

Stathopoulos A, Van Drenth M, Erives A, Markstein M, Levine M . Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell. 2002; 111(5):687-701. DOI: 10.1016/s0092-8674(02)01087-5. View

11.

Hekmat-Scafe D, Dang K, Tanouye M . Seizure suppression by gain-of-function escargot mutations. Genetics. 2005; 169(3):1477-93. PMC: 1449553. DOI: 10.1534/genetics.104.036558. View

12.

Landis G, Abdueva D, Skvortsov D, Yang J, Rabin B, Carrick J . Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2004; 101(20):7663-8. PMC: 419663. DOI: 10.1073/pnas.0307605101. View

13.

Hill A, Hunter C, Tsung B, Brown E . Genomic analysis of gene expression in C. elegans. Science. 2000; 290(5492):809-12. DOI: 10.1126/science.290.5492.809. View

14.

Bochdanovits Z, van der Klis H, de Jong G . Covariation of larval gene expression and adult body size in natural populations of Drosophila melanogaster. Mol Biol Evol. 2003; 20(11):1760-6. DOI: 10.1093/molbev/msg179. View

15.

Kendziorski C, Irizarry R, Chen K, Haag J, Gould M . On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci U S A. 2005; 102(12):4252-7. PMC: 552978. DOI: 10.1073/pnas.0500607102. View

16.

Egger B, Leemans R, Loop T, Kammermeier L, Fan Y, Radimerski T . Gliogenesis in Drosophila: genome-wide analysis of downstream genes of glial cells missing in the embryonic nervous system. Development. 2002; 129(14):3295-309. DOI: 10.1242/dev.129.14.3295. View

17.

Girardot F, Monnier V, Tricoire H . Genome wide analysis of common and specific stress responses in adult drosophila melanogaster. BMC Genomics. 2004; 5:74. PMC: 526417. DOI: 10.1186/1471-2164-5-74. View

18.

Adams M, Celniker S, Holt R, Evans C, Gocayne J, Amanatides P . The genome sequence of Drosophila melanogaster. Science. 2000; 287(5461):2185-95. DOI: 10.1126/science.287.5461.2185. View

19.

Dubnau J, Chiang A, Grady L, Barditch J, Gossweiler S, McNeil J . The staufen/pumilio pathway is involved in Drosophila long-term memory. Curr Biol. 2003; 13(4):286-96. DOI: 10.1016/s0960-9822(03)00064-2. View

20.

Zinke I, Schutz C, Katzenberger J, Bauer M, Pankratz M . Nutrient control of gene expression in Drosophila: microarray analysis of starvation and sugar-dependent response. EMBO J. 2002; 21(22):6162-73. PMC: 137192. DOI: 10.1093/emboj/cdf600. View