Skip to main content
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2003 Apr;4(2):208–215. doi: 10.1002/cfg.281

Global Analysis of Cell Type-Specific Gene Expression

David W Galbraith 1,
PMCID: PMC2447418  PMID: 18629131

Abstract

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

Full Text

The Full Text of this article is available as a PDF (169.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bachem C. W., van der Hoeven R. S., de Bruijn S. M., Vreugdenhil D., Zabeau M., Visser R. G. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J. 1996 May;9(5):745–753. doi: 10.1046/j.1365-313x.1996.9050745.x. [DOI] [PubMed] [Google Scholar]
  2. Brenner S., Johnson M., Bridgham J., Golda G., Lloyd D. H., Johnson D., Luo S., McCurdy S., Foy M., Ewan M. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol. 2000 Jun;18(6):630–634. doi: 10.1038/76469. [DOI] [PubMed] [Google Scholar]
  3. Brenner S., Williams S. R., Vermaas E. H., Storck T., Moon K., McCollum C., Mao J. I., Luo S., Kirchner J. J., Eletr S. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1665–1670. doi: 10.1073/pnas.97.4.1665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brown V., Jin P., Ceman S., Darnell J. C., O'Donnell W. T., Tenenbaum S. A., Jin X., Feng Y., Wilkinson K. D., Keene J. D. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell. 2001 Nov 16;107(4):477–487. doi: 10.1016/s0092-8674(01)00568-2. [DOI] [PubMed] [Google Scholar]
  5. Chalfie M., Tu Y., Euskirchen G., Ward W. W., Prasher D. C. Green fluorescent protein as a marker for gene expression. Science. 1994 Feb 11;263(5148):802–805. doi: 10.1126/science.8303295. [DOI] [PubMed] [Google Scholar]
  6. Che Ping, Gingerich Derek J., Lall Sonia, Howell Stephen H. Global and hormone-induced gene expression changes during shoot development in Arabidopsis. Plant Cell. 2002 Nov;14(11):2771–2785. doi: 10.1105/tpc.006668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chu Tzu Ming, Weir Bruce, Wolfinger Russ. A systematic statistical linear modeling approach to oligonucleotide array experiments. Math Biosci. 2002 Mar;176(1):35–51. doi: 10.1016/s0025-5564(01)00107-9. [DOI] [PubMed] [Google Scholar]
  8. Deyholos M. K., Galbraith D. W. High-density microarrays for gene expression analysis. Cytometry. 2001 Apr 1;43(4):229–238. [PubMed] [Google Scholar]
  9. Fei Y., Hughes T. E. Transgenic expression of the jellyfish green fluorescent protein in the cone photoreceptors of the mouse. Vis Neurosci. 2001 Jul-Aug;18(4):615–623. doi: 10.1017/s0952523801184117. [DOI] [PubMed] [Google Scholar]
  10. Feldman A. L., Costouros N. G., Wang E., Qian M., Marincola F. M., Alexander H. R., Libutti S. K. Advantages of mRNA amplification for microarray analysis. Biotechniques. 2002 Oct;33(4):906-12, 914. doi: 10.2144/02334mt04. [DOI] [PubMed] [Google Scholar]
  11. Galbraith D. W., Anderson M. T., Herzenberg L. A. Flow cytometric analysis and FACS sorting of cells based on GFP accumulation. Methods Cell Biol. 1999;58:315–341. doi: 10.1016/s0091-679x(08)61963-9. [DOI] [PubMed] [Google Scholar]
  12. Galbraith D. W., Harkins K. R., Maddox J. M., Ayres N. M., Sharma D. P., Firoozabady E. Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science. 1983 Jun 3;220(4601):1049–1051. doi: 10.1126/science.220.4601.1049. [DOI] [PubMed] [Google Scholar]
  13. Galbraith D. W., Herzenberg L. A., Anderson M. T. Flow cytometric analysis of transgene expression in higher plants: green fluorescent protein. Methods Enzymol. 1999;302:296–315. doi: 10.1016/s0076-6879(99)02028-5. [DOI] [PubMed] [Google Scholar]
  14. Harkins K. R., Jefferson R. A., Kavanagh T. A., Bevan M. W., Galbraith D. W. Expression of photosynthesis-related gene fusions is restricted by cell type in transgenic plants and in transfected protoplasts. Proc Natl Acad Sci U S A. 1990 Jan;87(2):816–820. doi: 10.1073/pnas.87.2.816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Haseloff J. GFP variants for multispectral imaging of living cells. Methods Cell Biol. 1999;58:139–151. doi: 10.1016/s0091-679x(08)61953-6. [DOI] [PubMed] [Google Scholar]
  16. Hawley T. S., Telford W. G., Ramezani A., Hawley R. G. Four-color flow cytometric detection of retrovirally expressed red, yellow, green, and cyan fluorescent proteins. Biotechniques. 2001 May;30(5):1028–1034. doi: 10.2144/01305rr01. [DOI] [PubMed] [Google Scholar]
  17. Kerr M. K., Martin M., Churchill G. A. Analysis of variance for gene expression microarray data. J Comput Biol. 2000;7(6):819–837. doi: 10.1089/10665270050514954. [DOI] [PubMed] [Google Scholar]
  18. Lagos-Quintana Mariana, Rauhut Reinhard, Yalcin Abdullah, Meyer Jutta, Lendeckel Winfried, Tuschl Thomas. Identification of tissue-specific microRNAs from mouse. Curr Biol. 2002 Apr 30;12(9):735–739. doi: 10.1016/s0960-9822(02)00809-6. [DOI] [PubMed] [Google Scholar]
  19. Macas J., Lambert G. M., Dolezel D., Galbraith D. W. Nuclear expressed sequence Tag (NEST) analysis: a novel means to study transcription through amplification of nuclear RNA. Cytometry. 1998 Dec 1;33(4):460–468. [PubMed] [Google Scholar]
  20. Martel Ralph R., Botros Ihab W., Rounseville Matthew P., Hinton James P., Staples Robin R., Morales David A., Farmer John B., Seligmann Bruce E. Multiplexed screening assay for mRNA combining nuclease protection with luminescent array detection. Assay Drug Dev Technol. 2002 Nov;1(1 Pt 1):61–71. doi: 10.1089/154065802761001310. [DOI] [PubMed] [Google Scholar]
  21. Nakajima K., Sena G., Nawy T., Benfey P. N. Intercellular movement of the putative transcription factor SHR in root patterning. Nature. 2001 Sep 20;413(6853):307–311. doi: 10.1038/35095061. [DOI] [PubMed] [Google Scholar]
  22. Nuwaysir Emile F., Huang Wei, Albert Thomas J., Singh Jaz, Nuwaysir Kate, Pitas Alan, Richmond Todd, Gorski Tom, Berg James P., Ballin Jeff. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 2002 Nov;12(11):1749–1755. doi: 10.1101/gr.362402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Pease A. C., Solas D., Sullivan E. J., Cronin M. T., Holmes C. P., Fodor S. P. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5022–5026. doi: 10.1073/pnas.91.11.5022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Sawamoto K., Yamamoto A., Kawaguchi A., Yamaguchi M., Mori K., Goldman S. A., Okano H. Direct isolation of committed neuronal progenitor cells from transgenic mice coexpressing spectrally distinct fluorescent proteins regulated by stage-specific neural promoters. J Neurosci Res. 2001 Aug 1;65(3):220–227. doi: 10.1002/jnr.1145. [DOI] [PubMed] [Google Scholar]
  25. Schena M., Shalon D., Davis R. W., Brown P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20;270(5235):467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  26. Sheen J. Signal transduction in maize and Arabidopsis mesophyll protoplasts. Plant Physiol. 2001 Dec;127(4):1466–1475. [PMC free article] [PubMed] [Google Scholar]
  27. Singh-Gasson S., Green R. D., Yue Y., Nelson C., Blattner F., Sussman M. R., Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974–978. doi: 10.1038/13664. [DOI] [PubMed] [Google Scholar]
  28. Takeuchi Yutaka, Yoshizaki Goro, Kobayashi Terumasa, Takeuchi Toshio. Mass isolation of primordial germ cells from transgenic rainbow trout carrying the green fluorescent protein gene driven by the vasa gene promoter. Biol Reprod. 2002 Oct;67(4):1087–1092. doi: 10.1095/biolreprod67.4.1087. [DOI] [PubMed] [Google Scholar]
  29. Velculescu V. E., Zhang L., Vogelstein B., Kinzler K. W. Serial analysis of gene expression. Science. 1995 Oct 20;270(5235):484–487. doi: 10.1126/science.270.5235.484. [DOI] [PubMed] [Google Scholar]
  30. Vos P., Hogers R., Bleeker M., Reijans M., van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995 Nov 11;23(21):4407–4414. doi: 10.1093/nar/23.21.4407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Wolfinger R. D., Gibson G., Wolfinger E. D., Bennett L., Hamadeh H., Bushel P., Afshari C., Paules R. S. Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol. 2001;8(6):625–637. doi: 10.1089/106652701753307520. [DOI] [PubMed] [Google Scholar]
  32. Xu W., Bak S., Decker A., Paquette S. M., Feyereisen R., Galbraith D. W. Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana. Gene. 2001 Jul 11;272(1-2):61–74. doi: 10.1016/s0378-1119(01)00516-9. [DOI] [PubMed] [Google Scholar]

Articles from Comparative and Functional Genomics are provided here courtesy of Wiley

RESOURCES