• Four broad-specificity probes were designed to target the small subunit rRNA of bacteria related to Eubacterium hallii , the recently reclassified Faecalibacterium prausnitzii (formerly Fusobacterium prausnitzii ) ( 9 ), Coprococcus eutactus , and Roseburia intestinalis clusters (Table 1 and Fig. 1 and 2 ). (asm.org)
  • Radiolabeled as opposed to fluorescently tagged oligonucleotides increased the sensitivity, whereas alteration of the template, oligonucleotides, salt, and thermostable DNA ligase concentrations increased the specificity for the detection of minority codons. (asm.org)
  • Although oligo FISH probes are central to many recently developed massively multiplexed and superresolution imaging methods, no dedicated computational utility exists to facilitate the design of such probes on the genome-wide scale. (pnas.org)
  • Here, we introduce a streamlined pipeline for the rapid, genome-scale design of oligo FISH probes and validate our approach by using conventional and superresolution imaging. (pnas.org)
  • Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. (pnas.org)
  • We demonstrate the scalability of our approach by performing genome-scale probe discovery in numerous model organism genomes and showcase the performance of the resulting probes with diffraction-limited and single-molecule superresolution imaging of chromosomal and RNA targets. (pnas.org)
  • 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)
  • 3. The method of claim 2, wherein selecting probes from the ranked group-specific candidate probes comprises, for each target, selecting the most conserved or least conserved probes representing that target until each target genome is represented by a predetermined number of probes. (patentsencyclopedia.com)
  • 2004). Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. (core.ac.uk)
  • The level of gene expression is typically summarized from a probe set composed of several 25 mer probes designed to span a target region based on a UniGene cluster. (biomedcentral.com)
  • Using this method, we found that probes containing multiple guanines in a row (G-stacks) have abnormal binding behavior compared with other probes, both in gene expression assays and genotyping assays using Affymetrix microarrays. (ucf.edu)
  • The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear. (mcw.edu)
  • An earlier report describing differentiating Th cells using an oligonucleotide array analysis led to the production of a large volume of data [ 15 ], but because of the experimental design the gene expression profile of Th2 cells remained obscure. (biomedcentral.com)
  • We show that an oligonucleotide microarray complemented by quantitative RT-PCR is an excellent method for gene expression profiling. (biomedcentral.com)
  • We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. (biomedcentral.com)
  • 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)
  • The first successful technique for de novo oligonucleotide synthesis on a chip was developed by Affymetrix (Santa Clara, CA) using photolithographic techniques borrowed from the semiconductor industry. (biomedcentral.com)
  • Converts Affymetrix probe level data to expression levels by summarizing the probe set values into one expression measure and a standard error for this summary. (rdrr.io)
  • Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. (biomedcentral.com)
  • 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)
  • This combination of primer/probe binding makes it less likely to generate a signal from a nonspecific product or from misannealing. (europeanmedical.info)
  • Common to all is the measurement of fluorescence increase over time, as well as the need for an individual fluorescently labelled probe (single or in combination with a primer) for each detection. (biomers.net)
  • Prepare primer-probe mix containing a final concentration of 20 uM each primer and 10 uM each probe listed above. (cdc.gov)
  • The internal region contains two universal PCR primer sites that are common to all MIPs as well as a probe-release site, which is usually a restriction site. (wikipedia.org)
  • 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)
  • Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index ," published in Nature Biotechnology , is the 2019 recipient of the OTS Paper of the Year Award , recognizing the most impactful paper in the field of oligonucleotide therapeutics. (yahoo.com)
  • The Young Investigator Award recognizes the outstanding achievements and contributions by a professional scientist in the field of oligonucleotide therapeutics who has recently received his or her doctoral degree. (yahoo.com)
  • The growing applications of ready-to-use synthesized oligonucleotides in therapeutics and a large number of manufacturers offering various customizations is likely to drive the synthesized oligonucleotides segment in the years ahead. (digitaljournal.com)
  • 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)
  • High affinity TFO binding makes the designed probes highly suitable for ex/in vivo applications. (jbsdonline.com)
  • Moreover, we found that these probes are much more likely to produce outliers when fitting the observed signals according to the positional dependent nearest neighbor model, which gives reasonable estimates of binding affinity for most other probes. (ucf.edu)
  • Knorre, D.G. and Vlassov, V.V. (1991) Reactive oligonucleotide derivatives as gene-targeted biologically active com- pounds and affinity probes. (scirp.org)
  • 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)
  • 1 µl of each test solution was added to 9 µl of water containing 1 ng of a 5 x 104 cpm single-stranded RNA probe and incubated overnight at 37°C. 5 µl of each reaction were electrophoresed on a 5% acrylamide/8 M urea gel and exposed to film overnight. (thermofisher.com)
  • Deoxynucleoside phosphorothioates were introduced into the deoxyoxanosine-containing oligonucleotide probes in order to increase the cleavage accuracy of endonuclease V on double-stranded DNA templates. (rsc.org)
  • Oligonucleotides can be made via enzymatic cleavage or more commonly by chemical synthesis with polymerases. (selectscience.net)