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Oligonucleotide Array Sequence AnalysisGene Expression ProfilingDNA, ComplementaryReverse Transcriptase Polymerase Chain ReactionGene Expression RegulationExpressed Sequence TagsRNA, MessengerCluster AnalysisNucleic Acid HybridizationGene Expression Regulation, NeoplasticReproducibility of ResultsGene ExpressionMicroarray AnalysisGene LibraryBase SequenceProtein Array AnalysisTranscription, GeneticRNAUp-RegulationPolymerase Chain ReactionCarbocyaninesRNA, NeoplasmTumor Cells, CulturedIn Situ HybridizationBlotting, NorthernImmunohistochemistryGene Expression Regulation, DevelopmentalCell Line, TumorAmino Acid SequenceTissue Array AnalysisTranscription FactorsGenomicsDown-RegulationQuality ControlComputational BiologyMultigene FamilyDNA PrimersSignal TransductionAlgorithmsGene DosageTumor Markers, BiologicalSensitivity and SpecificityBreast NeoplasmsGene Expression Regulation, PlantCell LineDNA-Binding ProteinsDNAGene AmplificationGenome, HumanSequence Analysis, DNAApoptosisModels, GeneticModels, StatisticalMice, Inbred C57BLTime FactorsPhenotypeCells, CulturedMolecular Sequence DataCell DivisionProstatic NeoplasmsLiverDNA, NeoplasmBlotting, WesternAdenocarcinomaCell DifferentiationOligonucleotide ProbesCell CyclePrognosisDNA ProbesProteinsEpithelial CellsBrainFibroblastsSequence Homology, Nucleic AcidSequence AlignmentDisease Models, AnimalDatabases, GeneticSoftwareDose-Response Relationship, DrugTranscriptomeChromosome MappingGenesTransfectionOrgan SpecificityRecombinant ProteinsOligonucleotidesMutationData Interpretation, StatisticalSpecies SpecificityNeoplasm ProteinsRestriction MappingAlternative SplicingGenes, PlantGenomeToxicogeneticsOpen Reading FramesProteomeExonsGene Regulatory NetworksGenome, Bacterial
Expressed genesHybridizationOligonucleotideComplementaryNormalization methodExperimentsClonesTissueSynthesisAnalysisAnalysesGenome-wideMRNA expressionLibrariesSequencesGene expression patternsAmplificationAffymetrixReferencesMicro-arrayFluorescenceTranscriptsTechnologyQuantitativeFluorescentThousands of genesSubstrateValidateMethodsPrimerPolySpatialIntensityGeneticSequenceProbesReverseSpeciesClinicalDiagnosticTherapyCellsDevelopmentTechniqueStudy
Expressed genes3
  • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. (statsci.org)
  • The data obtained from the microarray chip are analysed using various software tools to identify differentially expressed genes, detect DNA mutations, and identify genetic variations. (tutorialspoint.com)
  • These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
Hybridization7
  • Because dolphin RNA is often available in only limited amounts, the microarray will be validated using both direct labeling of mRNA (when sufficient amounts are available) and indirect labeling, in which the RNA is amplified prior to labeling and hybridization to the microarray. (vin.com)
  • A limitation of the use of this technology is that small specimens of human tissue, such as obtained by core needle or fine needle aspiration (FNA) biopsies, may not be sufficient for microarray hybridization using direct labelling protocols. (biomedcentral.com)
  • A very recent report used amino C6dT-modified random hexamers to prime cDNA synthesis in conjunction with aminoallyl-dUTP and increased fluorescence intensity enough such that as little as 1 μg of total RNA from cell lines gave sufficient signal for cDNA microarray hybridization [ 14 ]. (biomedcentral.com)
  • RNA amplification techniques have been developed to address the need for sufficient RNA from tiny specimen for microarray hybridization. (biomedcentral.com)
  • The microarray technology is based on the hybridization of labelled DNA or RNA molecules to complementary sequences that are immobilized on a solid substrate. (tutorialspoint.com)
  • The principle of DNA microarray technology is based on the hybridization of complementary sequences of nucleic acid molecules. (tutorialspoint.com)
  • The principle of DNA microarray is based on the hybridization of DNA strands. (tutorialspoint.com)
Oligonucleotide9
  • The 2 most common microarray technologies in use are the oligonucleotide microarrays and the robotically spotted complementary DNA (cDNA) microarrays. (medscape.com)
  • Oligonucleotide microarrays are manufactured by Affymetrix (Santa Clara, Calif) using photolithographic techniques. (medscape.com)
  • There are two main types of DNA microarrays: cDNA microarrays and oligonucleotide microarrays. (tutorialspoint.com)
  • Oligonucleotide microarrays are prepared by synthesizing oligonucleotides directly on the microarray chip. (tutorialspoint.com)
  • The two main types of DNA microarray are the cDNA microarray and the oligonucleotide microarray. (tutorialspoint.com)
  • The cDNA microarray uses complementary DNA as probes, while the oligonucleotide microarray uses short DNA sequences as probes. (tutorialspoint.com)
  • In a dual-label (two-color) cDNA or long-oligonucleotide microarray, these systematic biases are often manifested as an imbalance of measured fluorescent intensities corresponding to Sample A versus those corresponding to Sample B. Systematic biases also affect between-slide comparisons. (ox.ac.uk)
  • The genotyping thetic oligonucleotide or PCR product-based microarrays. (cdc.gov)
  • The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. (nih.gov)
Complementary6
  • The introduction of complementary DNA (cDNA) microarray technology in 1995 has helped to facilitate the identification and classification of DNA sequence information and the assignment of functions to these new genes by allowing investigators to analyze expression of thousands of genes simultaneously in a single experiment. (medscape.com)
  • Messenger RNA (mRNA) from the sample of interest can serve as a template for producing complementary DNA (cDNA) in the presence of a reverse transcriptase enzyme. (medscape.com)
  • The DNA microarray contains thousands of known DNA sequences that are complementary to the DNA of the sample being tested. (tutorialspoint.com)
  • The DNA from the sample binds to the complementary sequences on the microarray, and the amount of bound DNA is measured to determine the expression level of each gene in the sample. (tutorialspoint.com)
  • Libraries of silkmoth mRNA transcripts were collected and converted to complementary DNA (cDNA) for storage using reverse transcriptase in the late 1970s. (wikipedia.org)
  • Microarrays that measure the abundances of a defined set of transcripts via their hybridisation to an array of complementary probes were first published in 1995. (wikipedia.org)
Normalization method1
  • RESULTS: We present a neural network-based normalization method for correcting the intensity- and spatiality-dependent bias in cDNA microarray datasets. (ox.ac.uk)
Experiments3
  • Critical quality control tests produced satisfactory results for use of this microarray in biological experiments. (canada.ca)
  • Because of the complexity of the data sets generated by microarray experiments, the use of data-analysis software is essential. (medscape.com)
  • MOTIVATION: Microarray experiments are affected by numerous sources of non-biological variation that contribute systematic bias to the resulting data. (ox.ac.uk)
Clones5
  • Random Expressed Sequence Tag (EST) clones have been isolated and sequenced from dolphin Peripheral Blood Leukocyte (PBL) cDNA libraries. (vin.com)
  • Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). (biomedcentral.com)
  • Gene expression was studied by cDNA microarrray analyses using 4608 unique clones from liver-derived expressed sequence tag (EST) libraries fortified with clones of known liver genes representing ∼4000 genes. (houstonmethodist.org)
  • Screening for chromosomal imbalances by array CGH, whether using cDNA 23 or BAC clones, 24 has mainly been performed on cancer samples, 25- 30 which usually contain large gene dose alterations. (bmj.com)
  • Funding for 5' and 3' resequencing of TOM1 microarray clones was provided by INRA. (cornell.edu)
Tissue3
  • Microarrays may be used to assay gene expression within a single sample or to compare gene expression in 2 different cell types or tissue samples, such as in healthy versus diseased tissue. (medscape.com)
  • In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. (nih.gov)
  • Therefore, we have recently developed the tissue microarray (TMA) technology to efficiently test the clinical relevance of candidate genes. (karger.com)
Synthesis5
  • After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (genomicglossaries.com)
  • Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
  • Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)
  • Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)
  • Three specific modifications, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and N1-methylguanosine (m1G), are abundant in eukaryotic tRNAs and are particularly problematic for reverse transcriptases (RTs) by causing cDNA synthesis to stop or misincorporate. (cdc.gov)
Analysis10
Analyses2
  • Microarray analyses showed that many genes were altered in expression following both LPS and copper treatments in comparison to vehicle controls. (birmingham.ac.uk)
  • For M. tuberculosis , M. bovis , and the various cus sequence typing, restriction fragment length polymor- bacillus Calmette-Guérin daughter strains, genome-wide phism, and fi ngerprinting using variable number of tandem microarray analyses have identifi ed large sequence poly- repeats have shown an apparent lack of genetic diversity of morphisms ( 4 , 8 - 10 ). (cdc.gov)
Genome-wide2
  • The substantial genomic diversity, along gence of M. ulcerans from M. marinum , a well-known fi sh with a prototype microarray that covered a small portion of pathogen that can cause limited granulomatous skin infec- the genome, suggests that a genome-wide microarray will tions in humans ( 14 ). (cdc.gov)
  • Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. (nih.gov)
MRNA expression1
  • DNA microarrays make it possible to analyze the mRNA expression of thousands of genes simultaneously. (karger.com)
Libraries6
  • Two cDNA libraries from known health status dolphin PBL have been generated including an IL-2 and an LPS-stimulated cDNA library, respectively biased towards T and B-cell gene expression. (vin.com)
  • From the two cDNA-libraries 24,000 ESTs were collected and a total of 2200 unigenes have been sequenced and annotated ( www.marinegenomics.org ). (vin.com)
  • The 2200 unigenes from the EST collection and the 62 immune-function targeted genes, together with other genes randomly selected without sequencing from the cDNA libraries, have been amplified and used to construct a cDNA microarray representing 3700 dolphin genes in duplicate for a total of 7400. (vin.com)
  • Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
  • The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. (nih.gov)
  • Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. (nih.gov)
Sequences4
  • To address these, we have generated 67 535 ESTs predominately from Brassica seeds, analyzed these sequences, and identified 10 642 unigenes for the preparation of a targeted seed cDNA array. (canada.ca)
  • DNA microarrays are simply platforms that consist of small solid supports onto which the sequences from thousands of different genes are attached at fixed locations. (medscape.com)
  • This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. (medscape.com)
  • There are two key contemporary techniques in the field: microarrays, which quantify a set of predetermined sequences, and RNA-Seq, which uses high-throughput sequencing to record all transcripts. (wikipedia.org)
Gene expression patterns1
Amplification5
  • T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. (biomedcentral.com)
  • We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. (biomedcentral.com)
  • Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. (biomedcentral.com)
  • T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays. (biomedcentral.com)
  • The investigators reported that this approach achieved up to 80- fold molar amplification from nanogram quantities of cDNA. (genomicglossaries.com)
Affymetrix2
  • MA-plots for single channel microarray platforms such as Affymetrix are computed from the means and differences of log-expression values from two microarrays. (statsci.org)
  • Affymetrix GeneChip microarrays are a powerful tool to study global gene expression profiles and have been used on many species. (cambridge.org)
References1
  • Stu Borman, Chemical and Engineering News, Dec. 16, 2002 lists as highlights of 2002 http://pubs.acs.org/cen/coverstory/8050/8050chemhighlights5.html with references to the literature on polysaccharide and glycoconjugate microarrays, monosaccharide chips, natural and synthetic oligosaccharide arrays, and synthetic oligosaccharides in microtiter plate format. (genomicglossaries.com)
Micro-array1
  • 31, 32 In this report we used a cDNA micro-array and two BAC clone micro-arrays on 10 previously identified cases containing 16 cryptic chromosome aberrations, to test their performance for the detection of small imbalances. (bmj.com)
Fluorescence1
  • The microarray chip is scanned using a fluorescence scanner to measure the intensity of fluorescence at each spot on the chip. (tutorialspoint.com)
Transcripts2
  • Bovine mammary gene expression profiling using a cDNA microarray enhanced for mammary-specific transcripts. (sutterhealth.org)
  • More than 20 000 transcripts were detected in triplicate ovine skeletal muscle and liver samples, which is more than would be possible using the commercially available sheep-specific microarray. (cambridge.org)
Technology4
  • By screening specific genes related to the muscle growth of swine using cDNA microarray technology, a total of 5 novel genes (GF (growth factor) I, II, III, IV and V) were identified. (animbiosci.org)
  • In this article, we will discuss the principle, types, and steps involved in the DNA microarray technology. (tutorialspoint.com)
  • The technology involves the preparation of a microarray chip, which consists of a solid substrate, usually glass or silicon, with thousands or millions of immobilized DNA probes. (tutorialspoint.com)
  • A potentially powerful way to gain insight in the complex pathogenesis of rheumatoid arthritis (RA) and to classify arthritides has arisen from cDNA microarray technology, which provides the opportunity to determine differences in gene expression of a large portion of the genome in search of genes that are differently expressed between clinically diagnosed arthritides. (biomedcentral.com)
Quantitative2
Fluorescent4
Thousands of genes2
  • [ 5 ] Because a microarray can be used to examine the expression of hundreds or thousands of genes at once, it promises to revolutionize the way gene expression is examined. (medscape.com)
  • A DNA microarray is a tool used to measure the expression levels of thousands of genes simultaneously. (tutorialspoint.com)
Substrate2
  • The microarray chip is prepared by depositing DNA probes onto a solid substrate, usually a glass slide or silicon wafer. (tutorialspoint.com)
  • Epoxy Microarray Slides provide a uniform substrate for a variety of DNA/RNA-based diagnostic applications. (gracebio.com)
Validate3
  • The cDNA dolphin array will be used to analyze PBL RNA from captive and wild dolphins of known health status with the aim to validate and optimize the cDNA microarray as a sensitive and informative tool for dolphin health assessment. (vin.com)
  • We selected nine changing genes for absolute quantification of transcript copy numbers by real-time RT-PCR to validate microarray differential expression and to assess inter-individual variability in individual fishes. (birmingham.ac.uk)
  • DNA microarrays and TMAs provide a powerful approach to identify large numbers of new candidate genes, and rapidly validate their clinical impact in large series of human tumors. (karger.com)
Methods1
  • Our studies demonstrate the feasibility of obtaining potential molecular profile or fingerprint of anticancer drugs in cancer cells by cDNA microarray, which might yield further insights into the mechanisms of drug resistance and suggest alternative methods of treatment. (johnshopkins.edu)
Primer1
  • Total RNA was isolated from each of 30 single mouse sclera (n=30, 6 sclera each from 1-, 2-, 3-, 6-, and 8-week-old mice) and reverse-transcribed into cDNA using a T7-N 6 primer. (molvis.org)
Poly1
  • Typical microarray labelling procedures require 2-4 μg poly(A) + RNA or 25-50 μg total RNA per cDNA microarray. (biomedcentral.com)
Spatial2
  • A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data. (ox.ac.uk)
  • This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. (bioconductor.org)
Intensity1
  • The data produced from a microarray experiment typically constitute a long list of measurements of spot intensities and intensity ratios, generated either by a pair-wise comparison of 2 samples or by a comparison of several samples with a common control. (medscape.com)
Genetic1
  • Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. (nih.gov)
Sequence3
  • DNA microarrays take advantage of the major feature of the DNA double helix, the sequence complementarity of the two-paired strands, by using DNA capture probes which are the complement of the expressed target sequence (mRNA, cRNA or cDNA made from the mRNA). (ddw-online.com)
  • However, by using a pro- ulcerans, a human pathogen for which the fully assembled totype plasmid-based microarray that covered 10% of the and annotated genome sequence was not available at the genome, we found multiple genomic DNA deletions among time of the study. (cdc.gov)
  • They also found that the amplicons were similar in size distribution to the parent cDNA and showed sequence heterogeneity. (genomicglossaries.com)
Probes1
Reverse1
  • The cDNA fragments are prepared by reverse-transcribing mRNA molecules into cDNA using reverse transcriptase. (tutorialspoint.com)
Species1
  • This same method also has the potential to allow the study of other species where species-specific microarrays are not available or whose genomes have not been comprehensively characterised. (cambridge.org)
Clinical1
  • Microarray technologies are already increasingly being used in urologic research, and will also have a strong impact on clinical urology. (karger.com)
Diagnostic1
  • New technologies such as microarrays are not only important for fundamental research, but will also be useful for diagnostic, prognostic or therapeutic purposes in individual patients. (karger.com)
Therapy1
  • In recent exploratory regional therapy alone or by the addition of systemical studies, markers from microarray gene expression medical therapy with increased side effects and costs. (lu.se)
Cells1
  • We have used cDNA microarray to monitor the expression profiles of MCF-7 cells that are either transiently treated with doxorubicin or selected for resistance to doxorubicin. (johnshopkins.edu)
Development1
  • We take a look at the use of DNA microarray for gene expression or expression profiling and how DNA chips are used for drug discovery and development as a whole. (ddw-online.com)
Technique1
  • Surgical application of cDNA microarray technique. (nih.gov)
Study1
  • Microarrays are a significant advance because of their small size and are therefore useful when one wants to survey a large number of genes quickly or when the study sample is small. (medscape.com)