• This set of tracks shows the genomic positions of probes and targets from a full suite of in-solution-capture target enrichment exome kits for Next Generation Sequencing (NGS) applications. (ucsc.edu)
  • The captured genomic material must also be suitable for sequencing to a satisfactory depth of coverage for research on variant alleles and sensitive applications like copy number variation (CNV) detection. (idtdna.com)
  • The xGen Exome Hyb Panel v2 consists of 415,115 probes that spans a 34 Mb target region (19,433 genes) of the human genome and 39 Mb of probe space-the genomic regions covered by probes. (idtdna.com)
  • Early studies of DNA melting and reformation were carried out in aqueous solutions and yielded important information about the dependence of melting temperature (Tm) on the G+C composition and salt concentration, as well as information on the dependence of the rate of reassociation on the sequence complexity of the nucleic acid. (ddw-online.com)
  • Disclosed are materials and methods for performing multiplex assays for nucleic acids, in which a transponder is associated with the bead(s) forming the solid phase used in the assay, nucleic acid probes are bound to the surface of the particles, and data concerning the assay is encoded on the transponder. (justia.com)
  • This invention relates to materials and methods for detecting nucleic acids in samples and, more particularly, to solid phase assays wherein transponders are associated with the beads constituting the solid phase, nucleic acid probes are bound to the surface of the particles and data concerning the assay is encoded on the transponders. (justia.com)
  • In an electronically-indexed multiplex assay of this invention, two or more classes of transponders, each encoded with a different index number and constructed to bind a different nucleic acid sequence, are incubated with the sample in a single vessel. (justia.com)
  • After necessary washes, incubations and additions are performed, the solid phase is analyzed to detect a label indicative of binding of nucleic acid in the sample to the oligonucleotide on the transponder, such as fluorescence, color, radioactivity or the like. (justia.com)
  • developed the first microarray containing splice-junction oligonucleotides to analyze splice events in yeast [ 16 ]. (biomedcentral.com)
  • Due to global developmental delay, he had a chromosomal microarray analysis at 28 months. (hindawi.com)
  • In an attempt to adapt resequencing microarray technol- ceptibility, and viral escape from vaccine-elicited immu- ogy to surveillance and diagnostics, we developed the res- nity, continually surveying the genetic composition (i.e., piratory pathogen microarray (RPM) version 1 for primary sequence) of circulating and emerging variants is detection and sequence typing of 20 common respiratory necessary. (cdc.gov)
  • 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)
  • Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. (medscape.com)
  • This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. (medscape.com)
  • Because of the complexity of the data sets generated by microarray experiments, the use of data-analysis software is essential. (medscape.com)
  • The 2 most common microarray technologies in use are the oligonucleotide microarrays and the robotically spotted complementary DNA (cDNA) microarrays. (medscape.com)
  • Use of resequencing microarrays to Influenza viruses are a major cause of respiratory infec- detect single nucleotide polymorphisms and generate pri- tions in humans and result in substantial illness, death, mary sequences enables identification of genetic variants and economic problems throughout the world. (cdc.gov)
  • Genetic analysis includes procedures for genotyping, SNP (single nucleotide polymorphism) detection, strain identification and various other procedures. (ddw-online.com)
  • The index number may define the nucleotide sequence of the oligonucleotide deposited on the surface of the particle, the catalog number of a DNA fragment deposited on the particle, index numbers of chemical steps which were involved in the chemical synthesis of an oligonucleotide bound to the particle, or some other relevant characteristics of the deposited molecules. (justia.com)
  • Although we did not convincingly document co-evolutionary changes between RT and 5'-leader sequences, we identified a novel phenomenon, wherein positions 200 and 201 immediately downstream of the HIV-1 primer binding site exhibited an extraordinarily high likelihood of containing a nucleotide mixture. (bvsalud.org)
  • [ 5 ] They consist of a glass surface onto which oligonucleotides consisting of 25 bases are built a single nucleotide at a time. (medscape.com)
  • We hope to provide a concise review of the literature and genes involved within our deletion sequence in the hope that it will contribute to creating a phenotypic profile for this patient population. (hindawi.com)
  • As the sequencing and gene annotation projects of entire genomes of many species are headed towards completion (see, e.g. [13] ), massive mapping efforts in biology are now focused on how the genes interact. (lu.se)
  • Since genes are composed of a given alphabet (A, T, C, G) with fixed pairing properties A-T and C-G, probes can be constructed that attract gene transcripts extracted from cell tissues and cultures. (lu.se)
  • The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)
  • The sequence analysis of the 32-35,000 predicted genes indicates the there may be as many as 1,000 kinase or kinase-like genes. (ddw-online.com)
  • Analysis of gene expression can include measuring expression levels of a small set of genes to whole genome expression monitoring. (ddw-online.com)
  • To provide this increased depth of coverage and enable high multiplexing of samples, the xGen Exome Hyb Panel v2 targets only the coding sequences (CDS) of human coding genes in the RefSeq 109 database. (idtdna.com)
  • For example, single cell analysis allows for the direct measurement of gene expression kinetics, or for the unambiguous identification of co-regulated genes, even in the presence of de-synchronization and heterogeneity that could obscure population-averaged measurements. (justia.com)
  • 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)
  • In most cases, however, circulating strains, novel strains emerge sporadically this technology has relied on specific amplification of a because of reassortment in the segmented influenza RNA limited number of target sequences before hybridization, genome and have resulted in devastating influenza pan- thus restricting throughput and limiting final identification demics ( 1-3 ). (cdc.gov)
  • Random prime labeling yields high specific activity labeled DNA probe which can be used for all southern, northern and in situ hybridization studies. (genelink.com)
  • Even though these array-based methods are high-throughput, they are physically limited by probe density and suffer from noisy signals resulting from background noise due to cross hybridization and signal saturation [ 3 , 8 - 10 ]. (biomedcentral.com)
  • Existing methods for measuring transcript levels in single cells include RT-qPCR (1), single molecule counting using digital PCR (2) or hybridization probes (3, 4), and next generation sequencing (5). (justia.com)
  • The use of splice-junction oligonucleotides to analyze splice events was proposed as early as 1986, when Morgan and Ward used them to identify differential splice forms of minute virus in mice cDNA [ 14 ]. (biomedcentral.com)
  • 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)
  • Random Primers can be also used similar to using hexamers in cDNA synthesis in combination with oligo dT to yield more 5' end cDNA sequence. (genelink.com)
  • Thus, many of the basic functionalities for microfluidic single cell gene expression analysis have been demonstrated in isolation, including cell manipulation and trapping (9, 10), RNA purification and cDNA synthesis (11-13), and microfluidic qPCR (14) following off-chip cell isolation cDNA synthesis and preamplification. (justia.com)
  • The Global Oligonucleotide Synthesis Market Report offers this critical insight to enhance your business acumen and expedite strategic decision-making. (researchandmarkets.com)
  • It provides comprehensive market analysis, highlighting the escalating use of oligonucleotide synthesis in diverse fields ranging from human health management to molecular diagnostics and therapeutics. (researchandmarkets.com)
  • It delves into the growing demand for cancer-related therapies and how this has fueled the exploration of custom oligonucleotide synthesis in cancer research. (researchandmarkets.com)
  • Make informed, strategic decisions that will strengthen your presence in the oligonucleotide synthesis market. (researchandmarkets.com)
  • The global oligonucleotide synthesis market size is expected to reach USD 8.83 billion by 2030. (researchandmarkets.com)
  • The increasing usage of oligonucleotide synthesis in several field such as human health management, molecular diagnostics, and therapeutics have boosted the demand for this product thereby contributing to the market's revenue growth. (researchandmarkets.com)
  • This can be attributed to the large revenue share of oligonucleotide synthesis for production of PCR primers. (researchandmarkets.com)
  • Moreover, this has resulted in an increase in investments aiding to explore the potential application of custom oligonucleotide synthesis in cancer research. (researchandmarkets.com)
  • By product type, the reagents segment is anticipated to witness significant growth in the coming years as reagents have recurring demand and usage in the oligonucleotide synthesis process. (researchandmarkets.com)
  • IDT proprietary synthesis methods enable challenging probes-such as those with high GC and AT content-to be appropriately represented in the panel. (idtdna.com)
  • Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy. (biomedcentral.com)
  • Whole-transcriptome sequencing (RNA-seq) technology has emerged as a revolutionary platform for genome-wide quantification of mRNA transcripts. (biomedcentral.com)
  • The number of sequencing reads that map to each transcript is used to infer the abundance of mRNA molecules. (biomedcentral.com)
  • Because the locations of the probes are known, the intensity and pattern of the labeled mRNA can be used to measure the expression of the targeted gene. (medscape.com)
  • Gene Link stocks various oligo dT primers, oligo dT VN primer, Oligo dT T7 primer, random primers, including an array of fluorescent dye labeled primers for genetic analysis using florescent detecting instruments. (genelink.com)
  • Random Primers are a mixture of oligonucleotides representing all possible sequence for that size. (genelink.com)
  • Oligonucleotides are most widely used as PCR primers. (researchandmarkets.com)
  • In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. (biomedcentral.com)
  • The performance of this splice array was validated with artificial constructs for CDC6 , VEGF , and PCBP4 isoforms. (biomedcentral.com)
  • The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. (biomedcentral.com)
  • This report will focus in using DNA microarrays for the analysis of gene expression or expression profiling, and how DNA chips are used for drug discovery and development. (ddw-online.com)
  • Massively parallel experimental assays, particularly DNA microarrays and sequencing, have revolutionized genomics research in the last decades. (nature.com)
  • You can view Archer assays alongside IDT's xGen™ NGS portfolio to find the best next generation sequencing solution for your lab. (idtdna.com)
  • In recent years, powerful techniques for genome-wide identification and analysis of alternative splicing isoforms have been developed. (biomedcentral.com)
  • DNA and genome sequencing. (cdc.gov)
  • Exome sequencing targets only the protein-coding regions of the genome. (idtdna.com)
  • Short sequence reads are generated by either single-end or paired-end sequencing. (biomedcentral.com)
  • 5'-Leader variants were defined as positions where ≥20â % of next-generation sequencing (NGS) reads differed from the HXB2 sequence. (bvsalud.org)
  • A confocal scanner then reads the fluorescent intensity of each hybridized sequence in the array. (medscape.com)
  • Transcriptome analysis has enhanced our understanding of the molecular constituents of cells and tissues. (biomedcentral.com)
  • This technique enables the sequencing of all RNA molecules in a high-throughput manner. (biomedcentral.com)
  • In addition to iden- sequencing produces accurate data, the requirement for tification, this method provided primary sequence informa- knowledge of template sequences and the inability to tion, which suggested that distinct lineages of influenza quickly process multiple targets hinder its practical appli- viruses co-circulated during the 2004-2005 season, and cation in epidemiologic and diagnostic investigations. (cdc.gov)
  • This manufacturing process gives the xGen Exome Hyb Panel v2 a unique advantage over array-derived pools in which missing or truncated probes cannot be identified before sequencing. (idtdna.com)
  • Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. (biomedcentral.com)
  • All probes in the panel are manufactured under ISO 13485 standards, and then, mass spectrometry and dual quantification measurements of each probe are performed before they are pooled into the xGen Exome Hyb Panel v2. (idtdna.com)
  • Two of the most common uses of the DNA microarrays are genetic analysis and the analysis of gene expression. (ddw-online.com)
  • Considerable effort over the last decade has been directed towards developing integrated and scalable single cell genetic analysis on chip (7, 8). (justia.com)
  • 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)
  • Although these systems provide a high-throughput qPCR readout, they do not address the front end sample preparation and require single cell isolation by FACS or micropipette followed by off-chip processing and pre-amplification of starting template prior to analysis. (justia.com)
  • The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. (biomedcentral.com)
  • Our probes are designed using a new "capture-aware" algorithm and assessed with proprietary off-target analysis. (idtdna.com)
  • xGen NGS-made for whole exome sequencing. (idtdna.com)
  • The xGen Exome Hyb Panel v2 consists of 415,115 individually synthesized, 5' biotinylated, oligonucleotide probes. (idtdna.com)
  • Our xGen Exome Hyb Panel v2 consists of 5′ biotin-modified oligonucleotide probes that are individually synthesized and analyzed by electrospray ionization-mass spectrometry (ESI-MS) and optical density (OD) measurement. (idtdna.com)
  • Quantitative analysis of RNA on a massively parallel array (RNA-MaP) 21 , 23 starts with ssDNA sequencing libraries including an RNA polymerase promoter region, a stall sequence, and a variable region complementary to the desired RNA. (nature.com)
  • Gene expression analysis may uncover or facilitate answers to these questions as well as assist research and development and health care in several other ways. (ddw-online.com)
  • Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. (biomedcentral.com)
  • All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. (biomedcentral.com)
  • Cultures testing positive for Each tiled prototype sequence was selected to have an influenza A or B viruses were confirmed by using reverse intermediate level of sequence homology across a group of transcription-polymerase chain reaction (RT-PCR) analy- microbial or viral strains, which allowed for efficient sis with previously reported protocols ( 16,17 ). (cdc.gov)
  • In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. (nature.com)
  • In what follows we limit ourselves to the analysis of gene expression measurements obtained using microarrays with small spots of DNA fixed to glass slides. (lu.se)
  • The critical step of integrating all steps of single cell analysis into a robust system capable of performing measurements on large numbers of cells has yet to be reported. (justia.com)
  • As simultaneously identified and typed all component strains an alterative, high-density oligonucleotide resequencing of the trivalent FluMist intranasal vaccine. (cdc.gov)
  • However, they do not simultaneously and directly measure the affinity parameters relevant to biological function and are biased towards strongly binding sequences. (nature.com)
  • This process is repeated to build specific oligonucleotide sequences. (medscape.com)
  • Accordingly, a goal of microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. (justia.com)
  • Microfluidic systems provide numerous advantages for single cell analysis: economies of scale, parallelization and automation, and increased sensitivity and precision that comes from small volume reactions. (justia.com)
  • In particular, microfluidic qPCR devices (Biomark Dynamic Array, Fluidigm) have recently been applied to single cell studies (15, 16). (justia.com)
  • Methods: We sequenced 5'-leader positions 37-356 of paired plasma virus samples from 29 individuals developing the NRTI-resistance mutation M184V, 19 developing an NNRTI-resistance mutation, and 32 untreated controls. (bvsalud.org)
  • Typically when data are presented, the fluor- escent intensity from the tissue is pseudo-colored red and the intensity from the reference green, and the logarithmic ratio of background corrected red and green intensities for each gene (spot) is subject to analysis (see Fig. 1 ). (lu.se)
  • For proteins, no obvious such probe technique exists. (lu.se)
  • Dot blotting and dot hybridisation (4) evolved out of the filter hybridisation technique and provided the basic concept for DNA arrays. (ddw-online.com)
  • High-throughput sequencing-RNA affinity profiling (HiTS-RAP) 22 is conceptually similar to RNA-MaP, but uses the E. coli replication terminator protein Tus to stall the RNA polymerase after transcribing the variable section of the DNA library. (nature.com)
  • Because of the high proportion of mixtures at these positions, we analysed 5'-leader mixture frequencies in two additional datasets: five publications reporting 294 dideoxyterminator clonal GenBank sequences from 42 individuals and six National Center for Biotechnology Information (NCBI) BioProjects reporting NGS datasets from 295 individuals. (bvsalud.org)
  • Unfortunately, such devices do not allow for high throughput analysis due to the manual effort involved in operating the valving mechanisms. (justia.com)
  • Using such probes, one can obtain a fingerprint of the gene expression activity in a macroscopic sample. (lu.se)
  • After the DNA library is sequenced on the Illumina flow cell, it is enzymatically double stranded by extension of a 5′ biotinylated primer. (nature.com)
  • Though accepted as the gold-standard for measuring gene expression, this method is lower throughput and not amenable to perform global expression analyses. (biomedcentral.com)