• The 2 most common microarray technologies in use are the oligonucleotide microarrays and the robotically spotted complementary DNA (cDNA) microarrays. (medscape.com)
  • Here, we examined the expression of the HE4 gene and protein in a large series of normal and malignant adult tissues by oligonucleotide microarray and tissue microarray, respectively. (nature.com)
  • Finally, the pooling of DNA samples or multiplex PCR strategies for SNP genotyping have also been described in several microarray methods, such as the original arrayed primer extension (APEX) [ 9 - 12 ] or single base extension (SBE-tags) [ 13 , 14 ] assays. (hindawi.com)
  • The early expression profiles of these Trichoderma strains were studied after 20 h of incubation in the presence of tomato plants, using a high-density oligonucleotide (HDO) microarray, and compared to the profiles in the absence of plants. (microbiologyresearch.org)
  • The Affymetrix SNP microarray applies a combination of photolithography and combinatorial chemistry to directly synthesize oligonucleotides on a glass surface. (cd-genomics.com)
  • However, no sheep-specific Affymetrix GeneChip is currently available and the bovine array is fairly limited in its coverage and annotation. (cambridge.org)
  • The other paper presents a new multi-step algorithm used with the Affymetrix GeneChip(r) Human Mapping 500K Early Access SNP arrays. (analytica-world.com)
  • The short-oligonucleotide-based Affymetrix GeneChip ® arrays utilize multiple probes for each gene with an automated control for the experimental process from hybridization to quantification and thus provide reliable and comparable data [ 2 ]. (biomedcentral.com)
  • Data reduction is an issue because Affymetrix GeneChip oligonucleotide microarrays assay each target mRNA with a set of 11 to 16 pairs of 25-nucleotide DNA probes. (biomedcentral.com)
  • Oligonucleotide microarrays are manufactured by Affymetrix (Santa Clara, Calif) using photolithographic techniques. (medscape.com)
  • Here, we used oligonucleotide and tissue microarrays to survey HE4 gene and protein expression in a large group of malignant and normal tissues from adults. (nature.com)
  • Transcribed RNA levels are often measured by hybridization to microarrays of oligonucleotide probes, in which each transcript is represented by multiple probes. (biomedcentral.com)
  • In short, the behavior of oligonucleotide microarrays is not adequately explained by models that only consider base complementarity. (biomedcentral.com)
  • Use of the Affymetrix Human GeneChip array and genomic. (cambridge.org)
  • In this study, we demonstrate that gDNA-based probe selection on the Affymetrix Human U133+2 GeneChip array can be used to study gene expression profiles in sheep tissues. (cambridge.org)
  • This process is repeated to build specific oligonucleotide sequences. (medscape.com)
  • Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide, which acts as the capture sequence. (cd-genomics.com)
  • High-density oligonucleotide arrays were used to identify genes differentially expressed between high and low ERG expressers. (nih.gov)
  • The array was employed in a process known as comparative genomic hybridization (CGH), which involves tagging genomic DNA from two individuals and then co-hybridizing it to the array. (analytica-world.com)
  • We simultaneously identified multiple biological warfare agents in environmental samples by looking at specific probe responses after hybridization and response patterns of the multiplexed array. (cdc.gov)
  • While the probes were selected to avoid the formation of secondary structures, such structures were not completely eliminated and probably affected the hybridization efficiency, resulting in higher detection limits for some probes on the array. (cdc.gov)
  • For this, a functional genomic approach to embryogenesis has been developed that uses high-density oligonucleotide arrays for large-scale detection and quantification of gene expression. (unibas.ch)
  • In embryos raised under standard conditions, transcripts were detected for 37% of the 1,519 identified genes represented on the arrays, and highly reproducible quantification of gene expression was achieved in all cases. (unibas.ch)
  • These results demonstrate that high-density oligonucleotide arrays are sensitive, efficient, and quantitative instruments for the analysis of large scale gene expression in Drosophila embryos. (unibas.ch)
  • The scanner that records the intensity value is linked to digital image analysis software, which produces a color-coded image of the array, and a quantitative value is recorded for each target gene. (medscape.com)
  • Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
  • The array covers 93.7% of the euchromatic (gene-containing) regions of the human genome and substantially improves resolution over previous arrays. (analytica-world.com)
  • For example, in the case of arrays using multi-probe sets, such as Affymetrix GeneChips ® , we first have to derive a representative value of gene expression from the signals of individual probes ("low-level" analysis). (biomedcentral.com)
  • For gene-wide SNP genotyping, such as fine mapping or haplotyping of candidate regions we recommend NGS or array-based technologies. (cd-genomics.com)
  • These oligonucleotide arrays were used for quantitative transcript imaging of embryonically expressed genes under standard conditions and in response to heat shock. (unibas.ch)
  • Data from the array were assessed with a new algorithmic tool, called CNVfinder, which accurately and reliably identified CNVs in the human genome. (analytica-world.com)
  • Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. (analytica-world.com)
  • A multiplexed array was fabricated by distributing up to 18 different microsphere sensors into the optical fiber array with species-specific 50-mer DNA probes corresponding to 6 BWAs of interest ( Bacillus anthracis , Yersinia pestis , Francisella tularensis , Brucella melitensis , Clostridium botulinum , and vaccinia virus) and 1 BWA simulant, Bacillus thuringiensis kurstaki , with each organism represented by at least 2 probe sequences ( Table A1 ). (cdc.gov)
  • To ensure sensitive detection of BWAs with high accuracy, the performance of this multiplexed, high-density array was assessed by examining the detection limits and specificity of probes with Cy3-labeled synthetic targets (the synthetic target is a 50-mer oligonucleotide complementary to the probe). (cdc.gov)
  • Affymetrix arrays can achieve very high density to accommodate millions of probes on a single chip. (cd-genomics.com)
  • The specificity of the algorithm, coupled with the increased probe density of these arrays, permitted the identification of approximately 1,000 CNVs, many of which were below the detection size limit of alternative methodologies. (analytica-world.com)
  • To evaluate probe specificity, arrays containing beads with only a single probe type were exposed sequentially to the synthetic complementary target as well as to all noncomplementary targets. (cdc.gov)
  • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. (statsci.org)
  • The GoldenGate assay (Illumina, San Diego, Calif, USA) [ 7 , 8 ] is based on a similar principle but includes two oligonucleotides flanking the SNPs for the genotyping reactions. (hindawi.com)
  • The fact that the K α distributions are so close to t- distribution and independent of conditions and type of arrays suggests that the quantitative data provided by Affymetrix technology give "true" representation of physical processes, involved in measurement of RNA abundance. (biomedcentral.com)
  • A confocal scanner then reads the fluorescent intensity of each hybridized sequence in the array. (medscape.com)
  • The inherent redundancy of each probe type on the array, because each microsphere type has many replicates, provides additional confidence in detection and enhances the signal-to-noise ratio. (cdc.gov)
  • We developed a fiber-optic, microsphere-based, high-density array composed of 18 species-specific probe microsensors to identify biological warfare agents. (cdc.gov)
  • Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays , PLoS Computational Biology. (qiagenbioinformatics.com)
  • Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. (bvsalud.org)
  • By utilizing Affymetrix and Illumina array platforms, we support high-throughput, multiplex processing to meet diverse research needs. (cd-genomics.com)
  • An MA-plot of two-colour data is a representation of the data from one array. (statsci.org)
  • Dot blotting and dot hybridisation (4) evolved out of the filter hybridisation technique and provided the basic concept for DNA arrays. (ddw-online.com)
  • In contrast, the fiber-optic, microsphere-based, multiplexed arrays described in this paper can rapidly screen and simultaneously identify multiple potential BWAs, enabling an efficient response to a bioterrorism attack. (cdc.gov)
  • ink-jet oligonucleotide technology for synthesizing DNA and nanostring technology for analyzing single molecules of DNA and RNA. (wikipedia.org)
  • Removing noise and systematic biases is performed in order to both improve the biological signal and make all the arrays comparable. (biomedcentral.com)
  • For single-channel arrays one needs as least two arrays to make an MA-plot. (statsci.org)
  • Because the assembly process for the arrays is random, each bead type is encoded with an identifying optical bar code ( 11 , 12 ) created by entrapping dyes in various combinations within microspheres, to differentiate microsphere probe types from one another. (cdc.gov)
  • The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. (bvsalud.org)