title: Hybridization buffer systems impact the quality of filter array data.
abstract: BACKGROUND
  cDNA microarray technology has greatly facilitated mechanistic studies in pharmacology and toxicology. A clean hybridization with minimal background is critical for successful microarray analysis and is highly desired. However, clean hybridization alone is not enough; verification is needed.
  
  
  METHODS
  Total RNA was isolated from the livers of acetaminophen-intoxicated mice and was subjected to cDNA microarray analyses using ExpressHyb, ULTRArrayHyb or MicroHyb on nylon membranes. Real-time RT-PCR analyses were performed for verification.
  
  
  RESULTS
  We have demonstrated in this paper that hybridization systems can significantly impact the quality of array data. MicroHyb produced very clean hybridizations, but some results could not be confirmed by real-time RT-PCR and in accord with biological responses. The hybridization images from ExpressHyb were not always clean, but were reliable. The sensitivity of ULTRArrayHyb was moderate.
  
  
  CONCLUSIONS
  This study has indicated the importance of selecting hybridization buffers in membrane arrays and recommended real-time RT-PCR for follow-up analysis. Gene expression changes should also be correlated with biological significance.
authors.affiliation: Inorganic Carcinogenesis Section, LCC, NCI at NIEHS, 111 Alexander Drive, RTP, NC 27709, USA. Liu6@niehs.nih.gov
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.forename: Nigel
authors.initials: N
authors.lastname: Walker
authors.forename: Michael P
authors.initials: MP
authors.lastname: Waalkes
mesh_terms: D000082:Acetaminophen / Q000633:toxicity; D018712:Analgesics, Non-Narcotic / Q000633:toxicity; D000818:Animals; D002021:Buffers; D017931:DNA Primers; D008099:Liver / Q000187:drug effects* / Q000378:metabolism; D008297:Male; D051379:Mice; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D018712:Analgesics, Non-Narcotic; D002021:Buffers; D017931:DNA Primers; D012333:RNA, Messenger; D000082:Acetaminophen