Microarrays frozen

Yim SH, Ward JM, Dragan Y et al. Microarray analysis using amplified mRNA from laser capture microdissection of microscopic hepatocellular precancerous lesions and frozen hepatocellular carcinomas reveals unique and consistent gene expression profiles. Toxicol Pathol 2003-,31 295-303. 

Karsten SL, Van Deerlin VM, Sabatti C et al. An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res 2002 30 E4. 

Scicchitano MS, Dalmas DA, Bertiaux MA et al. Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. JHistochem Cytochem 2006 54 1229-1237. 

However, because of constraint of resources, sometimes toxicogenomics is not necessary if the sole purpose is to run a study in preclinical safety assessment it is more likely to piggyback on other toxicology conducts. At other times, a microarray study happens to run because of leftover of interested frozen tissues, a mere afterthought rather than a planned experiment. Such practice might confound the data interpretation and limit the future reference value of the study. As discussed earlier, the incremental value of toxicogenomics lies in the ever-expanding reference data of quality. 

Intrinsic gene set Molecular classification for all breast carcinomas c-DNA microarray Luminal A Luminal B ERBB2 Basal-like Normal breast-like Fresh/frozen NA... 

Seventy-six gene profile Prognostic for lymph node negative irrespective of HR status Oligonucleotide microarray Good prognosis versus Poor prognosis Fresh/frozen Rotterdam Assay-in development by Veridex, Warren, NJ)... 

Schoenberg Fejzo, M. and D. J. Slamon. 2001. Frozen tumor tissue microarray technology for analysis of tumor RNA, DNA, and proteins. Am J Pathol 159 1645-50. 

Methods are under development for analysis of protein from formalin-fixed tissues, although protein yield may be less than that from frozen tissue. Extraction of high-yield, quality protein from formalin-fixed tissue is generally difficult because of the extensive cross-links formed in formalin-fixed samples. Currently, the optimal tissue specimen for use with protein lysate microarrays is fresh tissue, immediately embedded in a cyroprotectant solution and frozen or snap-frozen tissue. 

The level of GAS colonization during infection is monitored by enumeration of CPUs from two of live throat swabs taken at various intervals from each of the infected animals during the infection protocol. Throat swabs are processed to release adherent bacteria and plated on select agar to minimize growth of resident microbial flora from the macaque posterior pharynx. The three remaining throat swabs are snap frozen and stored at -80 °C. Our laboratory freezes these three throat swabs for future use in expression microarray and/or quantitative PCR analyses to monitor GAS and/or host gene expression during upper respiratory tract infection (21,22). 

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