title: Identification of artifactual microarray probe signals constantly present in multiple sample types.
abstract: The detection, identification, and quantitation of transcripts have evolved from simple Northern analysis, cDNA cloning, and sequencing to RT-PCR, microarrays, and now digital gene expression using ultra-high-throughput RNA sequencing (RNA-Seq). During the course of our studies we observed that some microarray probes show very high signal intensity values yet are discordant when compared with RNA-Seq. A total of 99 probes from approximately 30,000 were identified as consistently discordant in four human tissues or cell lines. Interestingly, this set of discordant probes appears array-dependent. Among the 99 probes identified, 70 constantly exhibited a high signal in all 713 available samples surveyed using the Illumina HumanHT-12v4 platform. Some were discordant with additional probes that annotated the same genes. Absence of a number of these transcripts was confirmed by quantitative RT-PCR (qRT-PCR). Our findings suggest that one must be cautious, as some array probes do not capture the level of the target.
authors.affiliation: Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
authors.forename: Shihong
authors.initials: S
authors.lastname: Mao
authors.forename: Aletheia Lima
authors.initials: AL
authors.lastname: Souza
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Goodrich
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Krawetz
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D018076:DNA, Complementary / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D015341:Nucleic Acid Probes / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010920:Placenta / Q000378:metabolism; D011247:Pregnancy; D012313:RNA / Q000235:genetics* / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012867:Skin / Q000166:cytology; D013094:Spermatozoa / Q000378:metabolism; D013737:Testis / Q000378:metabolism
chemical_list: D018076:DNA, Complementary; D015341:Nucleic Acid Probes; D012313:RNA