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  • high
  • By using the very high information content inherent in high-density oligonucleotide arrays it will be possible to map the locations of RNA transcription along the length of the entire human genome. (ornl.gov)
  • DIG-labeled RNA probes are also stable for more than a year, making them ideal for long-term studies with high consistency and low technical variation. (selectscience.net)
  • microarray probe
  • YODA is an application primarily for selecting microarray probe sequences for measuring gene expression. (vt.edu)
  • At the time of its development, none of the existing programs for this task satisfied the best-known requirements for microarray probe selection. (vt.edu)
  • The question of what makes a good microarray probe was a research area at the time, and YODA was developed to incorporate the latest understanding of these requirements, drawn from the research literature, into a tool that can be used by a research biologist. (vt.edu)
  • genome
  • An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. (biomedcentral.com)
  • To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and additional probes are used only where necessary to span polymorphic regions of the genome. (biomedcentral.com)
  • An array providing unbiased coverage of probes across a genome is commonly referred to as a whole-genome tiling array . (biomedcentral.com)
  • Current designs select suitable probes through in silico scanning of transcriptome/genome based on first principles. (ucf.edu)
  • Probes are often derived from fragments of DNA that were isolated, purified, and amplified for use in the Human Genome Project. (wikipedia.org)
  • In the first schematic, a small segment of the genome is being detected by a DNA probe (thicker line). (wikipedia.org)
  • In allele "A", the genome is cleaved by a restriction enzyme at three nearby sites (triangles), but only the rightmost fragment will be detected by the probe. (wikipedia.org)
  • In the third schematic, the probe and restriction enzyme are chosen to detect a region of the genome that includes a variable number tandem repeat segment (boxes in schematic diagram). (wikipedia.org)
  • Affymetrix
  • For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software. (biomedcentral.com)
  • bind
  • Secondary antibodies (2o Ab) directed against the constant regions of the different primary antibodies, called PLA probes, bind to the primary antibodies. (wikipedia.org)
  • pairs
  • The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial communities using FISH followed by quantitative image analysis or real-time quantitative PCR, respectively. (biomedcentral.com)
  • These fragments are on the order of 100 thousand base-pairs, and are the basis for most FISH probes. (wikipedia.org)
  • A target-specific probe, composed of 20 oligonucleotide pairs, hybridizes to the target RNA(s). (wikipedia.org)
  • fragments
  • The probe hybridized with Southern blots of 0.5-kb HindIII-restricted chromosomal DNA fragments from all but five V. parahaemolyticus test isolates. (mysciencework.com)
  • specific
  • The sensitivity in detecting mature microRNAs by northern blots was increased by at least 10-fold compared to DNA probes, while simultaneously being highly specific, as demonstrated by the use of different single and double mismatched LNA probes. (pubmedcentralcanada.ca)
  • We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance. (biomedcentral.com)
  • A 26-mer oligonucleotide specific to Vibrio parahaemolyticus was synthesized from a 1,275-bp thermostable direct hemolysin (tdh) gene. (mysciencework.com)
  • minimal
  • In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. (biomedcentral.com)
  • fragment
  • In allele "a", restriction site 2 has been lost by a mutation, so the probe now detects the larger fused fragment running from sites 1 to 3. (wikipedia.org)
  • In allele "c" there are five repeats in the VNTR, and the probe detects a longer fragment between the two restriction sites. (wikipedia.org)
  • In allele "d" there are only two repeats in the VNTR, so the probe detects a shorter fragment between the same two restriction sites. (wikipedia.org)
  • Autoradiography
  • It requires a large amount of sample DNA, and the combined process of probe labeling, DNA fragmentation, electrophoresis, blotting, hybridization, washing, and autoradiography could take up to a month to complete. (wikipedia.org)
  • Different
  • In addition to Clostridium, we also analysed Bacteroides and Lactobacillus using previously described probes and the number or the frequency of occurrence of Bacteroides was shown to be different among mouse groups analysed. (semanticscholar.org)
  • applications
  • Broder, Graham R. , Ranasinghe, Rohan T. , Neylon, Cameron , Morgan, Hywel and Roach, Peter L. (2011) Kinetics and thermodynamics of biotinylated oligonucleotide probe binding to particle-immobilized avidin and implications for multiplexing applications. (soton.ac.uk)
  • five
  • Out of 689 samples, we observed five heteroplasmic samples (excluding the variable C-stretch beginning at position 303) using the immobilized SSO probe panel. (diva-portal.org)
  • In this study, five new oligonucleotide probes were designed and applied to detect these clostridial groups that are essential for the normalization of germfree mice. (semanticscholar.org)
  • These five new probes for mouse clostridia were able to detect the difference in clostridial diversity in each mouse group. (semanticscholar.org)
  • Short
  • Each of the PLA probes has a unique short DNA strand attached to it, If the PLA probes are in close proximity (that is, if the two original proteins of interest are in close proximity, or part of a protein complex, as shown in the figures), the DNA strands can participate in rolling circle DNA synthesis when appropriate substrates and enzymes are added. (wikipedia.org)
  • several
  • The SSO probe strips were used for the analysis of shed hairs and bloodstains from several criminal cases in Sweden, one of which is described here. (diva-portal.org)
  • Several wash steps remove all unhybridized or partially hybridized probes. (wikipedia.org)
  • analysis
  • FISH allows the analysis of a large series of archival cases much easier to identify the pinpointed chromosome by creating a probe with an artificial chromosomal foundation that will attract similar chromosomes. (wikipedia.org)
  • RFLP analysis may be subdivided into single- (SLP) and multi-locus probe (MLP) paradigms. (wikipedia.org)
  • provide
  • However, due to lack of tools, the observed microarray data have not been used to assess the performance of individual probes to provide feedback to improve future designs. (ucf.edu)
  • The oligonucleotides presented here provide a useful tool to study C. testosteroni population dynamics in mixed microbial communities. (biomedcentral.com)