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PMID: 15123585 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

A versatile assay for high-throughput gene expression profiling on universal array matrices.

Genome research ·Vol. 14 ·No. 5 ·2004-05-00 ·Pages 878-85

Fan JB, Yeakley JM, Bibikova M, Chudin E, Wickham E, Chen J, Doucet D, Rigault P, Zhang B, Shen R, McBride C, Li HR, Fu XD, Oliphant A, Barker DL, Chee MS

Abstract

We report a flexible, sensitive, and quantitative gene-expression profiling system for assaying more than 400 genes, with three probes per gene, for 96 samples in parallel. The cDNA-mediated annealing, selection, extension and ligation (DASL) assay targets specific transcripts, using oligonucleotides containing unique address sequences that can hybridize to universal arrays. Cell-specific gene expression profiles were obtained using this assay for hormone-treated cell lines and laser-capture microdissected cancer tissues. Gene expression profiles derived from this assay were consistent with those determined by qRT-PCR. The DASL assay has been automated for use with a bead-based 96-array matrix system. The combined high-throughput assay and readout system is accurate and efficient, and can cost-effectively profile the expression of hundreds of genes in thousands of samples.

MeSH Terms
Androgens/pharmacology Animals Cell Line Cell Line, Tumor DNA, Complementary/biosynthesis,genetics Gene Expression Profiling/methods Gene Expression Regulation/drug effects,genetics Humans Lasers Male Mice Microdissection/methods Oligonucleotide Array Sequence Analysis/methods Organ Specificity/drug effects,ethics,genetics Prostatic Neoplasms/metabolism,pathology RNA/genetics,metabolism Reverse Transcriptase Polymerase Chain Reaction/methods Sensitivity and Specificity
Chemicals
Androgens DNA, Complementary RNA
Authors & Affiliations
16 authors, click to expand affiliations / ORCID
Fan Jian-Bing
Illumina, Inc., San Diego, California 92121, USA. jfan@illumina.com
Yeakley Joanne M
Bibikova Marina
Chudin Eugene
Wickham Eliza
Chen Jing
Doucet Dennis
Rigault Philippe
Zhang Baohong
Shen Richard
McBride Celeste
Li Hai-Ri
Fu Xiang-Dong
Oliphant Arnold
Barker David L
Chee Mark S
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.2167504
Email
jfan@illumina.com
Published
2004-05-00
Pages
878-85
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC479115
Subset
IM
Grants
NCI NIH HHS · R33 CA088351 · United States
NCI NIH HHS · R33 CA88351 · United States
NCI NIH HHS · R44 CA83398 · United States
External Links
PubMed source DOI: 10.1101/gr.2167504 PMC Full Text View journal details
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