A method for automated detection of gene expression required for the establishment of a digital transcriptome-wide gene expression atlas

Journal of Microscopy

Volumn 217, Issue 3, 2005, Pages 275-281

  Carson, James P ^a   Eichele, G ^b   Chiu, W ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Catalysed report deposition (CARD) signal amplification; Detecting gene expression; Non radioactive in situ hybridization; Transcriptomics

Indexed keywords

CELL CULTURE; CELL PROLIFERATION; THROUGHPUT; TISSUE;

AUTOMATED DETECTION; CATALYZED REPORT DEPOSITION SIGNAL AMPLIFICATION; DETECTING GENE EXPRESSION; GENES EXPRESSION; HIGH-THROUGHPUT; IN-SITU HYBRIDIZATION; NON-RADIOACTIVE IN SITU HYBRIDIZATION; SIGNAL AMPLIFICATIONS; TRANSCRIPTOMES; TRANSCRIPTOMICS;

GENE EXPRESSION;

TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; AUTOANALYSIS; BRAIN; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SCREENING; IN SITU HYBRIDIZATION; MOUSE; NONHUMAN; PRIORITY JOURNAL;

EID: 14744299104     PISSN: 00222720     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2818.2005.01450.x     Document Type: Article

References (20)

1. Asan, E. & Kugler, P. (1995) Qualitative and quantitative detection of alkaline phosphatase coupled to an oligonucleotide probe for somatostatin mRNA after in situ hybridization using unfixed rat brain tissue. Histochem. Cell Biol. 103, 463-471.
2. Benali, A., Leefken, I., Eysel, U.T. & Weiler, E. (2003) A computerized image analysis system for quantitative analysis of cells in histological brain sections. J. Neurosci. Methods, 125, 33-43.
3. Bobrow, M.N., Harris, T.D., Shaughnessy, K.J. & Litt, G.J. (1989) Catalyzed reporter deposition, a novel method of signal amplification. Application to immunoassays. J. Immunol. Methods, 125, 279-285.
4. Carson, J.P. (2004) Quantitative annotation and analysis of gene expression patterns with an atlas of the mouse brain. PhD thesis, Baylor College of Medicine, Houston.
5. Carson, J.P., Ju, T., Thaller, C., Warren, J., Bello, M., Kakadiaris, I., Chiu, W. & Eichele, G. (2004) Automated characterization of gene expression patterns with an atlas of the mouse brain. Proceedings of the 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, San Francisco, pp. 2917-2920.
6. Carson, J.P., Thaller, C. & Eichele, G. (2002) A transcriptome atlas of the mouse brain at cellular resolution. Curr. Opin. Neurobiol. 12, 562-565.
7. Castleman, K.R. (1996) Digital Image Processing. Prentice Hall, Englewood Cliffs, NJ.
8. Emson, P.C. (1993) In-situ hybridization as a methodological tool for the neuroscientist. Trends Neurosci. 16, 9-16.
9. Hashimoto, N., Yamanaka, H., Mizushima, T. & Noguchi, K. (2003) Increased expression of 3 beta-hydroxysteroid dehydrogenase mRNA in dorsal root ganglion neurons of adult rats following peripheral nerve injury. Neurosci. Lett. 340, 45-48.
10. Ju, T., Warren, J., Eichele, G., Thaller, C., Chiu, W. & Carson, J. (2003) A geometric database for gene expression data. Eurographics Symposium on Geometry Processing (ed. by L. Kobbelt, P. Schröder & H. Hoppe), pp. 166-176. Eurographics Association, Aachen, Germany.
11. Kerstens, H.M., Poddighe, P.J. & Hanselaar, A.G. (1995) A novel in situ hybridization signal amplification method based on the deposition of biotinylated tyramine. J. Histochem. Cytochem. 43, 347-352.
12. Noguchi, K., Morita, Y., Kiyama, H., Sato, M., Ono, K. & Tohyama, M. (1989) Preproenkephalin gene expression in the rat spinal cord after noxious stimuli. Brain Res. Mol. Brain Res. 5, 227-234.
13. Reymond, A., Marigo, V., Yaylaoglu, M.B., Leoni, A., Ucla, C., Scamuffa, N., Caccioppoli, C., Dermitzakis, E.T., Lyle, R., Banfi, S., Eichele, G., Antonarakis, S.E. & Ballabio, A. (2002) Human chromosome 21 gene expression atlas in the mouse. Nature, 420, 582-586.
14. Ruifrok, A. (1996) Quantification of immunohistochemical staining by color translation and automated thresholding. Anal. Quant. Cytol. Histol. 19, 107-113.
15. Russ, J.C. (2002) The Image Processing Handbook. CRC Press, Boca Raton, FL.
16. Speel, E.J. (1999) Robert Feulgen Prize Lecture 1999. Detection and amplification systems for sensitive, multiple-target DNA and RNA in situ hybridization: looking inside cells with a spectrum of colors. Histochem. Cell Biol. 112, 89-113.
17. Visel, A., Thaller, C. & Eichele, G. (2004) GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 32, D552-D556.
18. Wang, H. & Wessendorf, M.W. (2002) Mu- and delta-opioid receptor mRNAs are expressed in periaqueductal gray neurons projecting to the rostral ventromedial medulla. Neuroscience, 109, 619-634.
19. Wessendorf, M.W., Wang, H. & Schnell, S.A. (2004) Statistical methods for in situ hybridization: identification of autoradiographically labelled cells and structures. J. Microsc. 215, 50-61.
20. Zreiqat, H., Sungaran, R., Howlett, C.R. & Markovic, B. (1998) Quantitative aspects of an in situ hybridization procedure for detecting mRNAs in cells using 96-well microplates. Mol Biotechnol. 10, 107-113.