2004
DOI: 10.1038/nbt948
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Expression profiling using a hexamer-based universal microarray

Abstract: We describe a transcriptional analysis platform consisting of a universal micro-array system (UMAS) combined with an enzymatic manipulation step that is capable of generating expression profiles from any organism without requiring a priori species-specific knowledge of transcript sequences. The transcriptome is converted to cDNA and processed with restriction endonucleases to generate low-complexity pools (approximately 80-120) of equal length DNA fragments. The resulting material is amplified and detected wit… Show more

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Cited by 32 publications
(26 citation statements)
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“…Microarray analysis was performed with the GenCompass universal microarray system (Agilix Corporation, New Haven, Conn.). The specific details of this technology have been described recently (33). The data reference the UniGene database Build 161 (National Center for Biotechnology Information, Bethesda, Md.).…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Microarray analysis was performed with the GenCompass universal microarray system (Agilix Corporation, New Haven, Conn.). The specific details of this technology have been described recently (33). The data reference the UniGene database Build 161 (National Center for Biotechnology Information, Bethesda, Md.).…”
Section: Methodsmentioning
confidence: 99%
“…)-or ethidium bromide (Sigma)-stained gels. For quantitative real-time PCRs (qPCRs), primers and probes were designed with Beacon Designer 2.06 (Premier Biosoft International, Palo Alto, Calif.), and analyses were performed using the MX400 Multiplex Quantitative PCR system (Stratagene, La Jolla, Calif.) as previously described (33). Primers and probes for all analyses are available upon request.…”
Section: Methodsmentioning
confidence: 99%
“…The 5 end-phosphorylated 33-mer is designed to fold into itself to form a 10-bp stem, a 4-base loop, and a single-stranded 9-base 3 extension containing a degenerate hexamer region with Cy5 blocking the terminal 3 end. These partial single-stranded target mixtures mimic the annealed targets for ligation to hexamer microarrays in the universal microarray system (UMAS) (9). …”
Section: Methodsmentioning
confidence: 99%
“…The sum of all pixel intensities were captured per spot, and averages were calculated from triplicate spots in the array. For a test of microarray probe functionality, ligation reactions were carried out as previously described (9). A 33-mer Cy5-labeled degenerate hairpin oligonucleotide (Integrated DNA Technologies) was used as a surrogate target mixture.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation