Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 15123585

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

Jian-Bing Fan·Joanne M Yeakley·Marina Bibikova·Eugene Chudin·Eliza Wickham·Jing Chen·Dennis Doucet·Philippe Rigault·Baohong Zhang·Richard Shen·Celeste McBride·Hai-Ri Li·Xiang-Dong Fu·Arnold Oliphant·David L Barker·Mark S Chee
View original source ↗Export metadata ↓

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.

Explore related subjects

AndrogensAnimalsCell LineCell Line, TumorDNA, ComplementaryGene Expression ProfilingGene Expression RegulationHumansLasersMaleMiceMicrodissectionOligonucleotide Array Sequence AnalysisOrgan SpecificityProstatic NeoplasmsRNAReverse Transcriptase Polymerase Chain ReactionSensitivity and SpecificityComparative StudyJournal ArticleResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jian-Bing Fan, Joanne M Yeakley, Marina Bibikova, Eugene Chudin, Eliza Wickham, Jing Chen, Dennis Doucet, Philippe Rigault, Baohong Zhang, Richard Shen, Celeste McBride, Hai-Ri Li, Xiang-Dong Fu, Arnold Oliphant, David L Barker, Mark S Chee. 2004. A versatile assay for high-throughput gene expression profiling on universal array matrices.. https://doi.org/10.1101/gr.2167504

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2016

Androgen-sensitive hypertension associated with soluble guanylate cyclase-α1 deficiency is mediated by 20-HETE.

Dysregulated nitric oxide (NO) signaling contributes to the pathogenesis of hypertension, a prevalent and often sex-specific risk factor for cardiovascular disease. We previously reported that mice deficient in the α1-subunit of the NO receptor soluble guanylate cyclase (sGCα1 (-/-) mice) display sex- and strain-specific hypertension: male but not female sGCα1 (-/-) mice are hypertensive on an 129S6 (S6) but not a C57BL6/J (B6) background. We aimed to uncover the genetic and molecular basis of the observed sex- and strain-specific blood pressure phenotype. Via linkage analysis, we identified a suggestive quantitative trait locus associated with elevated blood pressure in male sGCα1 (-/-)S6 mice. This locus encompasses Cyp4a12a, encoding the predominant murine synthase of the vasoconstrictor 20-hydroxy-5,8,11,14-eicosatetraenoic acid (20-HETE). Renal expression of Cyp4a12a in mice was associated with genetic background, sex, and testosterone levels. In addition, 20-HETE levels were higher in renal preglomerular microvessels of male sGCα1 (-/-)S6 than of male sGCα1 (-/-)B6 mice. Furthermore, treating male sGCα1 (-/-)S6 mice with the 20-HETE antagonist 20-hydroxyeicosa-6(Z),15(Z)-dienoic acid (20-HEDE) lowered blood pressure. Finally, 20-HEDE rescued the genetic background- and testosterone-dependent impairment of acetylcholine-induced relaxation in renal interlobar arteries associated with sGCα1 deficiency. Elevated Cyp4a12a expression and 20-HETE levels render mice susceptible to hypertension and vascular dysfunction in a setting of sGCα1 deficiency. Our data identify Cyp4a12a as a candidate sex-specific blood pressure-modifying gene in the context of deficient NO-sGC signaling.

Androgens↗
PubMed2005

Androgen receptor corepressors: an overview.

Androgens play pivotal roles in sex differentiation and development, in reproductive functions, and sexual behavior. The actions of androgens are mediated through the intracellular androgen receptor (AR), a member of the nuclear receptor (NR) superfamily, which regulates a wide range of target gene expression. Recent studies indicate that the proper transcriptional activity of AR is modulated by AR coregulators, including coactivators that can enhance AR transactivation and corepressors that can suppress AR transactivation. Here, we summarize the recent discoveries relating to AR corepressor function with the following different mechanisms: (1) corepressors that inhibit the DNA binding or nuclear translocation of AR; (2) corepressors that recruit histone deacetylases; (3) corepressors that interrupt the interaction between AR and its coactivators; (4) corepressors that interrupt the interaction between the N-terminus and C-terminus of AR; (5) corepressors that function as scaffolds for other AR coregulators; (6) corepressors that target the basal transcriptional machinery; (7) other mechanisms. The potential impact and future directions of AR corepressors are also discussed.

Androgens↗
PubMed2005

Establishment and characterization of a human primary prostate carcinoma cell line, HH870.

BACKGROUND: Development of new therapeutic modalities for human prostate carcinoma has been impeded by a lack of adequate in vitro and in vivo models. Most in vitro studies have been carried out using a limited number of human prostate cancer cell lines that are mostly derived from metastatic tumors sites or are immortalized. METHODS: Characterization of the prostate cancer cell line, HH870, included description of morphology, determination of doubling time, response to androgens, immunocytochemistry, and immunoblotting of proteins known to be associated with prostate carcinoma, karyotyping, fluorescence in situ hybridization (FISH), DNA profiling, and growth as xenograft in athymic rodents. RESULTS: HH870 expresses various epithelial marker antigens that correlate with known basic immunostaining profiles of prostate adenocarcinoma, although the cell line does not express PSA, PSMA, or PAP. HH870 exhibits complex chromosomal abnormalities and harbors no immortalizing HPV, BKV, JCV, and SV40 DNA. CONCLUSIONS: We report the successful establishment and characterization of a new long-term primary human prostate tumor cell line HH870.

Androgens↗