Collection of epithelial cells from rodent mammary gland via laser capture microdissection yielding high-quality RNA suitable for microarray analysis

Biological Procedures Online

Volumn 12, Issue 1, 2010, Pages 31-43

  McGinley, John N ^a   Zhu, Zongjian ^a   Jiang, Weiqin ^a   Thompson, Henry J ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

Laser capture microdissection; Mammary epithelial cells; RNA quality

Indexed keywords

RNA;

ADIPOCYTE; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BREAST ADENOCARCINOMA; CONTROLLED STUDY; DEHYDRATION; EPITHELIUM CELL; FEMALE; GENETIC ANALYSIS; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; LASER CAPTURE MICRODISSECTION; MAMMARY GLAND; NONHUMAN; PROCESS OPTIMIZATION; QUALITY CONTROL; RAT; RNA HYBRIDIZATION; RNA ISOLATION; RNA PROBE; RNA PROCESSING; SIGNAL NOISE RATIO; STROMA CELL; TISSUE MICROARRAY;

RODENTIA;

EID: 78649833464     PISSN: 14809222     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12575-010-9026-8     Document Type: Article

References (31)

1. Erickson HS, Gillespie JW, Emmert-Buck MR (2008) Tissue microdissection. Methods Mol Biol 424:433-448
2. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
3. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW (1996) Parallel human genome analysis: microarray-based expression mon-itoring of 1000 genes. Proc Natl Acad Sci USA 93:10614-10619
4. Simone NL, Bonner RF, Gillespie JW, Emmert-Buck MR, Liotta LA (1998) Laser-capture microdissection: opening the microscopic frontier to molecular analysis. Trends Genet 14:272-276
5. Wheelan SJ, Martinez MF, Boeke JD (2008) The incredible shrinking world of DNA microarrays. Mol Biosyst 4:726-732
6. Sarder P, Nehorai A, Davis PH, Stanley SL (2008) Estimating gene signals from noisy microarray images. IEEE Trans Nanobioscience 7:142-153
7. Balogh GA, Heulings R, Mailo D, Wang R, Li YS, Hardy R et al (2007) Methodological approach to study the genomic profile of the human breast. Int J Oncol 31:253-260
8. Domazet B, Maclennan GT, Lopez-Beltran A, Montironi R, Cheng L (2008) Laser capture microdissection in the genomic and proteomic era: targeting the genetic basis of cancer. Int J Clin Exp Pathol 1:475-488
9. Kabbarah O, Pinto K, Mutch DG, Goodfellow PJ (2003) Expression profiling ofmouse endometrial cancers microdissected from ethanol-fixed, paraffin-embedded tissues. Am J Pathol 162:755-762
10. Espina V, Wulfkuhle JD, Calvert VS, VanMeter A, Zhou W, Coukos G et al (2006) Laser-capture microdissection. Nat Protoc 1:586-603
11. Specht K, Richter T, Muller U, Walch A, Werner M, Hofler H (2001) Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 158:419-429
12. Srinivasan M, Sedmak D, Jewell S (2002) Effect offixatives and tissue processing on the content and integrity ofnucleic acids. Am JPathol 161:1961-1971
13. Goldsworthy SM, Stockton PS, Trempus CS, Foley JF, Maronpot RR (1999) Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue. Mol Carcinog 25:86-91
14. Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K (1999) Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 27:4436-4443
15. Cox ML, Schray CL, Luster CN, Stewart ZS, Korytko PJ, MK KN et al (2006) Assessment of fixatives, fixation, and tissue processing on morphology and RNA integrity Exp Mol Pathol 80:183-191
16. Gugic D, Nassiri M, Nadji M, Morales A, Vincek V (2007) Novel tissue preservative and tissue fixative for comparative pathology and animal research. J Exp Anim Sci 43:271-281
17. Vincek V, Nassiri M, Nadji M, Morales AR (2003) A tissue fixative that protects macromolecules (DNA, RNA, and protein) and histomorphology in clinical samples. Lab Invest 83:1427-1435
18. Wang H, Owens JD, Shih JH, Li MC, Bonner RF, Mushinski JF (2006) Histological staining methods preparatory to laser capture microdissection significantly affect the integrity of the cellular RNA. BMC Genomics 7:97
19. Mikulowska-Mennis A, Taylor TB, Vishnu P, Michie SA, Raja R, Horner N et al (2002) High-quality RNA from cells isolated by laser capture microdissection. Biotechniques 33:176-179
20. Sluka P, O'Donnell L, McLachlan RI, Stanton PG (2008) Application of laser-capture microdissection to analysis of gene expression in the testis. Prog Histochem Cytochem 42:173-201
21. Kerman IA, Buck BJ, Evans SJ, Akil H, Watson SJ (2006) Combining laser capture microdissection with quantitative real-time PCR: effects of tissue manipulation on RNA quality and gene expression. J Neurosci Methods 153:71-85
22. Upson JJ, Stoyanova R, Cooper HS, Patriotis C, Ross EA, Boman B et al (2004) Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection. J Cell Physiol 201:366-373
23. Leiva IM, Emmert-Buck MR, Gillespie JW (2003) Handling of clinical tissue specimens for molecular profiling studies. Curr Issues Mol Biol 5:27-35
24. Zhu Z, Jiang W, McGinley JN, Price JM, Gao B, Thompson HJ (2007) Effects of dietary energy restriction on gene regulation in mammary epithelial cells. Cancer Res 67:12018-12025
25. Thompson HJ, McGinley JN, Rothhammer K, Singh M (1995) Rapid induction of mammary intraductal proliferations, ductal carcinoma in situ and carcinomas by the injection of sexually immature female rats with 1-methyl-1-nitrosourea. Carcinogenesis 16:2407-2411
26. Chu S (2009) IR laser capture vs UV laser cutting choice based on experimental objective. In: LCM Protocols and Techniques. http://www. moleculardevices.com/pdfs/LCM-Users-Meeting/Day2/Chu-LCM-users-meeting- Protocols-050609.pdf, accessed 1 Dec. 2009
27. Chen Z, McGee M, Liu Q, Scheuermann RH (2007) A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics 23:321-327
28. McGee M, Chen Z (2006) Parameter estimation for the exponential-normal convolution model for background correction of affymetrix GeneChip data. Stat Appl Genet Mol Biol 5: Article24
29. Singh R, Maganti RJ, Jabba SV, Wang M, Deng G, Heath JD et al (2005) Microarray-based comparison of three amplification methods for nanogram amounts of total RNA. Am J Physiol Cell Physiol 288:C1179-C1189
30. Affymetrix, Inc. (2004) Data analysis fundamentals. In: Gene-Chip® Expression Analysis. http://www.affymetrix.com/support/downloads/manuals/data- analysis-fundamentals-manual.pdf, accessed 4 Dec. 2009
31. Weis S, Llenos IC, Dulay JR Elashoff M, Martinez-Murillo F, Miller CL (2007) Quality control for microarray analysis of human brain samples: the impact of postmortem factors, RNA characteristics, and histopathology. JNeurosci Methods 165:198-209