title: A PCR-based approach to assess genomic DNA contamination in RNA: Application to rat RNA samples.
abstract: Genomic DNA (gDNA) contamination of RNA samples can lead to inaccurate measurement of gene expression by reverse transcription quantitative real-time PCR (RT-qPCR). We describe an easily adoptable PCR-based method where gDNA contamination in RNA samples is assessed by comparing the amplification of intronic and exonic sequences from a housekeeping gene. Although this alternative assay was developed for rat RNA samples, it could be easily adapted to other species. As a proof of concept, we assessed the effects of detectable gDNA contamination levels on the expression of a few genes that illustrate the importance of RNA quality in acquiring reliable data.
authors.affiliation: Hazard Identification Division, HECSB, Health Canada, Tunney's Pasture, Ottawa, Ontario, K1A 0L2, Canada. Electronic address: bhaja.krushna.padhi@hc-gc.gc.ca.
authors.forename: Bhaja K
authors.initials: BK
authors.lastname: Padhi
authors.affiliation: Hazard Identification Division, HECSB, Health Canada, Tunney's Pasture, Ottawa, Ontario, K1A 0L2, Canada.
authors.forename: Manjeet
authors.initials: M
authors.lastname: Singh
authors.affiliation: Hazard Identification Division, HECSB, Health Canada, Tunney's Pasture, Ottawa, Ontario, K1A 0L2, Canada.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Huang
authors.affiliation: Hazard Identification Division, HECSB, Health Canada, Tunney's Pasture, Ottawa, Ontario, K1A 0L2, Canada.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Pelletier
mesh_terms: D000818:Animals; D002531:Cerebellum / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D059018:DNA Contamination; D003851:Deoxyribonucleases / Q000378:metabolism; D042963:Electron Transport Complex II / Q000235:genetics; D015870:Gene Expression; D005821:Genetic Techniques; D008297:Male; D012313:RNA / Q000032:analysis* / Q000302:isolation & purification; D051381:Rats; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D012313:RNA; D004247:DNA; D042963:Electron Transport Complex II; D003851:Deoxyribonucleases
keywords: Gene expression; Genomic DNA contamination; Pseudogene; RNA quality; Rat; Sdha