title: Screening for control genes in rat global cerebral ischemia using high-density oligonucleotide array.
abstract: From conventional relative gene expression analyses (Northern blotting, in situ hybridization, and RT-PCR), it has been reported that the expression of control genes, such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-actin, used as references may be affected by ischemia. Therefore, we extended searching and evaluation at the mRNA level of transcripts whose expression levels were not changed by cerebral ischemia, using a high-density oligonucleotide array and statistical analysis in a rat global cerebral ischemia and reperfusion model. We added a hyperthermic factor and localization factor to ischemia and identified transcripts with a stable expression level under conditions even more disadvantageous than ischemia only. Screening of more than 8,000 transcripts with the Rat Genome U34A array yielded 28 transcripts, which we listed and classified according to their expression level. Widely used control genes, GAPDH and beta-actin, were not included, although cyclophilin A was included. In addition, we conducted a functional classification based on gene ontology. Under the functional classification of the 28 transcripts, many genes tended to be associated with metabolism. In conclusion, use of several transcripts is recommended, such as those we identified, as references in the analysis of gene expression in pathological models of ischemia.
authors.affiliation: Division of Genetic and Genomic Medicine, Advanced Medical Research Center, Nihon University School of Medicine, Oyaguchi-Kami Machi, Itabashi-ku, Tokyo, Japan.
authors.forename: Megumi Sugahara
authors.initials: MS
authors.lastname: Kobayashi
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Toshihito
authors.initials: T
authors.lastname: Nagata
authors.forename: Yayoi
authors.initials: Y
authors.lastname: Nishida
authors.forename: Akiko
authors.initials: A
authors.lastname: Murata
authors.forename: Koichi
authors.initials: K
authors.lastname: Ishikawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Asai
mesh_terms: D000818:Animals; D002545:Brain Ischemia / Q000235:genetics*; D005334:Fever / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D008297:Male; D008403:Mass Screening; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000378:metabolism; D051381:Rats; D017208:Rats, Wistar; D013194:Staining and Labeling
chemical_list: D012313:RNA