Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues

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dc.contributor.authorÖzdag, Hilal
dc.contributor.authorIDhttp://orcid.org/0000-0001-7940-2499tr_TR
dc.contributor.departmentBiyoteknoloji Enstitüsütr_TR
dc.contributor.otherBelder, Nevin
dc.contributor.otherCoşkun, Öznur
dc.date.accessioned2020-05-06T06:55:41Z
dc.date.available2020-05-06T06:55:41Z
dc.date.issued2016
dc.description.abstractFormalin-fixed paraffin-embedded (FFPE) tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013) [1]; Scicchitano et al., Scicchitano et al. (2006) [2]; Frank et al., Frank et al. (2007) [3]; Fedorowicz et al., Fedorowicz et al. (2009) [4]). However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO) database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples.tr_TR
dc.description.indexwos
dc.description.indexScopus
dc.identifier.endpage306tr_TR
dc.identifier.startpage303tr_TR
dc.identifier.urihttps://doi.org/10.1016/j.gdata.2016.02.006tr_TR
dc.identifier.urihttp://hdl.handle.net/20.500.12575/71214
dc.identifier.volume7tr_TR
dc.language.isoentr_TR
dc.relation.isversionof10.1016/j.gdata.2016.02.006tr_TR
dc.relation.journalGenomics Datatr_TR
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıtr_TR
dc.subjectFFPEtr_TR
dc.subjectGene expressiontr_TR
dc.subjectMicroarraytr_TR
dc.subjectOptimizationtr_TR
dc.titleOptimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissuestr_TR
dc.typeArticletr_TR

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