title: Screening for control genes in mouse hippocampus after transient forebrain ischemia using high-density oligonucleotide array.
abstract: In conventional relative gene expression analysis (Northern blotting, RT-PCR, and in situ hybridization), housekeeping genes such as the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta-actin genes, whose expression levels are considered stable, have been used as control genes for normalization of RNA quantitation. However, it has been reported that the expression levels of these two control genes are affected by ischemia. Therefore, we have been searching for novel control genes whose expression levels are stable in a mouse model of transient forebrain ischemia. Using the GeneChip Mu6500 array set, we monitored the expression levels of approximately 6000 murine genes in the mouse hippocampus during 24 h of ischemia-reperfusion. To select stable genes, we applied the restricted criterion of a 1.5-fold change in expression level as the threshold. By adding statistical analysis with this criterion, we identified 10 genes as candidates for control genes from the GeneChip data. In this criterion, GAPDH and beta-actin genes were not included in the 10 genes as candidates for control genes. The present findings might be relevant to the use of control genes in quantitation of RNA, particularly in the study of mouse transient forebrain ischemia.
authors.affiliation: Division of Genomic Epidemiology and Clinical Trials, Nihon University School of Medicine, Oyaguchi-Kamimachi, Tokyo, Japan.
authors.forename: Yayoi
authors.initials: Y
authors.lastname: Nishida
authors.forename: Megumi
authors.initials: M
authors.lastname: Sugahara-Kobayashi
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Toshihito
authors.initials: T
authors.lastname: Nagata
authors.forename: Koichi
authors.initials: K
authors.lastname: Ishikawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Asai
mesh_terms: D000818:Animals; D004195:Disease Models, Animal; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D006624:Hippocampus / Q000378:metabolism*; D002546:Ischemic Attack, Transient / Q000235:genetics*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016548:Prosencephalon; D012313:RNA / Q000378:metabolism
chemical_list: D012313:RNA