Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

By Timothy R. Hughes, M. Mao, Allan R. Jones, J. Burchard, M. Marton, K. Shannon, S. Lefkowitz, M. Ziman, Janell M. Schelter, Michael R. Meyer and 14 more. Nature Biotechnology, 2001

1,364 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b69e372acc662d6ea92ecfc991d42e3a835a2c14

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Citations in the corpus

Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells*S (2004, methodology): “Expression Profiling Using DNA Microarray—The mouse oligonucleotide microarrays (Agilent Technologies, Palo Alto, CA) that contain 23,574 oligonucleotides (60-mer) corresponding to 22,788 mouse genes were hybridized with cDNAs labeled with Cy3 or Cy5 (CyDye; Amersham Pharmacia Biotech, Piscataway, N”
Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. (2006, methodology): “All microarray experiments including data analysis were carried out as described previously (Hughes et al. 2001).”
Gene expression profiling predicts clinical outcome of breast cancer (2002, methodology): “Two hybridizations were carried out for each tumour using a fluorescent dye reversal technique on microarrays containing approximately 25,000 human genes synthesized by inkjet technolog”
Overexpression of spermidine synthase enhances tolerance to multiple environmental stresses and up-regulates the expression of various stress-regulated genes in transgenic Arabidopsis thaliana. (2004, methodology): “The synthesized cDNA was labeled by reaction with dye (NHS-ester Cy3 or Cy5; Amersham Biosci., U.S.A.) according to the method described by Hughes et al. (2001).”
STATISTICAL METHODS FOR IDENTIFYING DIFFERENTIALLY EXPRESSED GENES IN REPLICATED cDNA MICROARRAY EXPERIMENTS (2002, background): “…are several types of microarray systems, including the cDNA microarrays developed in the Brown and Botstein labs at Stanford (DeRisi et al. (1997), Hughes et al. (2001)) and the high-density oligonucleotide chips from the Affymetrix company (Lockhart et al. (1996)); the brief description below…”
From Boolean to probabilistic Boolean networks as models of genetic regulatory networks (2002, background): “The advent of cDNA microarrays and oligonucleotide chips [1, 2, 3, 4, 5], which facilitate large-scale surveys of gene expression, has incited much interdisciplinary scientific activity.”
CTLA-4 and PD-1 Receptors Inhibit T-Cell Activation by Distinct Mechanisms (2004, methodology): “Methods for mRNA amplification using in vitro transcription, cRNA labeling with Cy3 and Cy5, and hybridization have been described previously ( 30 ).”
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. (2003, background): “Recent work has shown that microarrays of 60mer oligonucleotides can reach a sensitivity level close to one copy of mRNA per human cell and that a single oligonucleotide per gene is suf®cient to monitor gene expression (2).”
A new approach to decoding life: systems biology. (2001, background): “Two types of arrays are in common use: cDNA microarrays (102) and oligonucleotide arrays (47, 66).”
Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. (2006, methodology): “Error models have been described previously (Hughes et al. 2001).”
Distinct requirements for the naturally occurring splice forms Stat4α and Stat4β in IL‐12 responses (2003, methodology): “Microarray analysis was carried out using arrays with ~24 000 murine genes at Rosetta Inpharmatics fabricated using their inkjet oligonucleotide synthesizer technology (Hughes et al., 2001).”
An integrative genomics approach to infer causal associations between gene expression and disease (2005, methodology): “To select a probe for each gene sequence, we used a series of filtering steps, taking into account repeat sequences, binding energies, base composition, distance from the 3′ end, sequence complexity and potential crosshybridization interaction”