title: Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization.
abstract: The aim of this work was to compare DNA microarray results using either total RNA or affinity-purified poly(A) RNA from the same biological sample for target preparation. The high-density oligonucleotide microarrays of both Agilent Technologies (based on two-color detection) and Applied Biosystems (based on single-color detection) were evaluated. Real-time quantitative PCR was used to quantify messenger RNA (mRNA) and ribosomal RNA (rRNA) at different stages of target preparations. Poly(A) RNA versus total RNA target hybridizations exhibited slightly lower correlation coefficients than did self versus self hybridizations (i.e., poly(A) RNA targets vs. poly(A) RNA targets or total RNA targets vs. total RNA targets). Only a small fraction of all transcripts appeared to be significantly over- or underrepresented when total RNA targets or poly(A) RNA targets from the same biological sample were compared. Therefore, the conclusion is that poly(A) affinity purification from total RNA can be omitted during target preparation for routine mRNA expression analysis using high-density oligonucleotide microarrays. Among consistently overrepresented transcripts in total RNA targets were histone mRNAs known to lack poly(A) tails. Therefore, structurally exceptional RNA species can be identified by comparing targets derived from either poly(A) RNA or total RNA using microarray hybridization.
authors: Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, N-5008 Bergen, Norway.
authors: Kjell
authors: K
authors: Petersen
authors: Anne Margrete
authors: AM
authors: Oyan
authors: Kari
authors: K
authors: Rostad
authors: Sue
authors: S
authors: Olsen
authors: Trond Hellem
authors: TH
authors: Bø
authors: Helga B
authors: HB
authors: Salvesen
authors: Bjørn Tore
authors: BT
authors: Gjertsen
authors: Oystein
authors: O
authors: Bruserud
authors: Ole Johan
authors: OJ
authors: Halvorsen
authors: Lars Andreas
authors: LA
authors: Akslen
authors: Vidar M
authors: VM
authors: Steen
authors: Inge
authors: I
authors: Jonassen
authors: Karl-Henning
authors: KH
authors: Kalland
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D002846:Chromatography, Affinity; D017931:DNA Primers / Q000235:genetics; D003851:Deoxyribonucleases; D016889:Endometrial Neoplasms / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics; D008297:Male; D009838:Oligodeoxyribonucleotides; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D011470:Prostatic Hyperplasia / Q000235:genetics; D012313:RNA / Q000235:genetics* / Q000302:isolation & purification; D012333:RNA, Messenger / Q000235:genetics* / Q000302:isolation & purification; D012334:RNA, Neoplasm / Q000235:genetics / Q000302:isolation & purification; D012335:RNA, Ribosomal / Q000235:genetics / Q000302:isolation & purification
chemical_list: D017931:DNA Primers; D009838:Oligodeoxyribonucleotides; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D012335:RNA, Ribosomal; C027903:oligo (dT); D012313:RNA; D003851:Deoxyribonucleases