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  • silico
  • 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 . (pubmedcentralcanada.ca)
  • Despite the diversity of platforms, ultimately they all use genomic DNA from disrupted cells to recreate a high resolution karyotype in silico. (wikipedia.org)
  • detect
  • This method may also be adapted to detect DNA methylation differences, as seen in Methylation-Sensitive Representational Difference Analysis (MS-RDA). (wikipedia.org)
  • To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology 1 . (jove.com)
  • For known exRNA nucleotide sequences, RT-PCR can be applied to detect their presence within a sample as well as quantify their abundance. (wikipedia.org)
  • The method of sequencing cDNA to find transcribed genes also runs into problems, such as failing to detect rare or very short RNA molecules, and so do not detect genes that are active only in response to signals or specific to a time frame. (wikipedia.org)
  • situ
  • Cyanine dyes are commonly used for fluorescent labeling of DNA and RNA oligonucleotides in applications including qPCR, sequencing, fluorescence in situ hybridization, Förster resonance energy transfer, and labeling for microarray hybridization. (jove.com)
  • (e) A nucleic-acid-containing solid support - the DNA chip or microarray - is obtained either by spotting cDNA clones or by in situ synthesis of oligonucleotides onto a glass surface. (nih.gov)
  • This technique was originally developed for the evaluation of the differences between the chromosomal complements of solid tumor and normal tissue, and has an improved resoIution of 5-10 megabases compared to the more traditional cytogenetic analysis techniques of giemsa banding and fluorescence in situ hybridization (FISH) which are limited by the resolution of the microscope utilized. (wikipedia.org)
  • They can be classified and distinguished according to various characteristics: Probe type: DNA arrays can comprise either mechanically spotted cDNAs or PCR-products, mechanically spotted oligonucleotides, or oligonucleotides that are synthesized in situ. (wikipedia.org)
  • Proteomic
  • Brief Funct Genomic Proteomic. (wikipedia.org)
  • Degradomics is a sub-discipline of biology encompassing all the genomic and proteomic approaches devoted to the study of proteases, their inhibitors, and their substrates on a system-wide scale. (wikipedia.org)
  • encodes
  • The cynS gene that encodes cyanase was identified among bacterial, fungal, and plant sequences in public databases, and the gene was particularly prevalent among cyanobacteria, including numerous Prochlorococcus and Synechococcus strains. (embl-heidelberg.de)
  • Transcriptome
  • We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. (biomedcentral.com)
  • Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. (bcgsc.ca)
  • In recent years several technologies for the complete analysis of the transcriptome and proteome have reached a technological level which allows their routine application as scientific tools. (hindawi.com)
  • This approach, however, needs technologies which facilitate the concurrent analysis of a large scale of the genome, the transcriptome, or the proteome in diseased versus nondiseased tissues (Figure 1 ). (hindawi.com)
  • Numerous studies have utilized microarray analysis to follow host cell transcriptome alterations in response to interactions with bacteria. (bio-medicine.org)
  • Tiling arrays aid in transcriptome mapping as well as in discovering sites of DNA/protein interaction (ChIP-chip, DamID), of DNA methylation (MeDIP-chip) and of sensitivity to DNase (DNase Chip) and array CGH. (wikipedia.org)
  • Traditional methods of gene prediction for annotation of genomic sequences have had problems when used to map the transcriptome, such as not producing an accurate structure of the genes and also missing transcripts entirely. (wikipedia.org)
  • In addition, proteases recruited from remote sources like nearby tissues are ignored by these DNA based arrays, reiterating the need for protein based methods to confirm the presence and activity of functional enzymes when transcriptome analysis is performed. (wikipedia.org)
  • RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. (wikipedia.org)
  • nucleic acid
  • Here, we show that DY547 and DY647, two alternative cyanine dyes that are becoming widely used for nucleic acid labeling, have a similar pattern of sequence-dependence, with adjacent purines resulting in higher intensity and adjacent cytosines resulting in lower intensity. (jove.com)
  • In a less formal way, bioinformatics also tries to understand the organisational principles within nucleic acid and protein sequences, called proteomics. (wikipedia.org)
  • Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. (wikipedia.org)
  • The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. (wikipedia.org)
  • quantification
  • The principle of these methods is the identification and quantification of up to ten thousands of RNA and proteins species in a tissue, in contrast to the sequential analysis of conventional methods such as PCR and Western blotting. (hindawi.com)
  • Traditional analytical tools for quantification of DNA, RNA, or proteins are restricted to the sequential analysis of one biomolecule specimen at a time. (hindawi.com)
  • In addition to detecting previously unidentified genes and regulatory sequences, improved quantification of transcription products is possible. (wikipedia.org)
  • The microbeads are then arrayed in a flow cell for sequencing and quantification. (wikipedia.org)
  • protein
  • Gene expression analysis is most simply described as the study of the way genes are transcribed to synthesize functional gene products - functional RNA species or protein products. (bio-rad.com)
  • Gene expression analysis studies can be broadly divided into four areas: RNA expression, promoter analysis, protein expression, and post-translational modification. (bio-rad.com)
  • Structural analysis of the protein suggests that Annexin VII is a membrane binding protein with diverse properties including voltage-sensitive calcium channel activity, ion selectivity and membrane fusion. (wikipedia.org)
  • This includes the analysis of the mutational DNA status and the RNA and protein expression levels of these specific genes to elucidate their role in the disease. (hindawi.com)
  • It also plays a role in the analysis of gene and protein expression and regulation. (wikipedia.org)
  • This includes nucleotide and amino acid sequences, protein domains, and protein structures. (wikipedia.org)
  • For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (wikipedia.org)
  • Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis. (wikipedia.org)
  • It also suffers from the same limitation of microarray analysis regarding the lack of correlation between transcript and protein levels. (wikipedia.org)
  • bioinformatics
  • Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. (wikipedia.org)
  • transcriptomes
  • However, because no method has existed to isolate bacterial RNA away from host cell RNA, the corresponding analyses of bacterial transcriptomes has been impossible. (bio-medicine.org)
  • In 2008, two human transcriptomes, composed of millions of transcript-derived sequences covering 16,000 genes, were published and, by 2015, transcriptomes had been published for hundreds of individuals. (wikipedia.org)
  • fragments
  • Since driver and tester sequences are nearly identical, the excess of driver DNA fragments will anneal to homologous DNA fragments from the tester species. (wikipedia.org)
  • As more cycles of RDA are performed, the pool of unique sequence fragment copies will grow faster than fragments found in both species. (wikipedia.org)
  • Saleembhasha, A;Mishra, Seema 2018-01-01 00:00:00 Abstract Powerful next-generation sequencing (NGS) technologies, more specifically RNA sequencing (RNA-seq), have been pivotal toward the detection and analysis and hypotheses generation of novel biomolecules, long noncoding RNAs (lncRNAs), tRNA-derived fragments (tRFs) and circular RNAs (circRNAs). (deepdyve.com)
  • In 1995, one of the earliest sequencing-based transcriptomic methods was developed, Serial Analysis of Gene Expression (SAGE), which worked by Sanger sequencing of concatenated random transcript fragments. (wikipedia.org)
  • computational
  • GiRaF is a computational tool for identification of reassortments in influenza viruses from sequence databases of isolates. (umd.edu)
  • In this review, starting from a brief relevant introduction to NGS and RNA-seq and the expression and role of lncRNAs, tRFs and circRNAs in cancer, we have comprehensively analyzed the current landscape of databases developed and computational software used for analyses and visualization for this emerging and highly interesting field of these novel biomolecules. (deepdyve.com)
  • Using NGS, thousands of sequences can be deciphered in a 'concurrent' manner and computational analyses done at a 'genome-wide' scale. (deepdyve.com)
  • RNA-SeQC RNA-SeQC is a tool with application in experiment design, process optimization and quality control before computational analysis. (wikipedia.org)
  • tissue
  • Genomic characterization of 51 MPNST tissue samples identified several frequently amplified regions harboring 2,599 genes and regions of deletion including 4,901 genes. (aacrjournals.org)
  • (c) High-quality RNA is then obtained from the tissue and subjected to quantitation and integrity analysis. (nih.gov)
  • In a particular type of cell or tissue, only a small subset of an organism's genomic DNA will be expressed as mRNAs at any given time. (wikipedia.org)
  • probe
  • In spotted cDNA arrays, the ratio of the two fluorophores is measured and the relative intensity of each probe is then calculated for each cDNA-containing spot. (nih.gov)
  • Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and washing after hybridization. (wikipedia.org)
  • Instead of probing for sequences of known or predicted genes that may be dispersed throughout the genome, tiling arrays probe intensively for sequences which are known to exist in a contiguous region. (wikipedia.org)
  • These arrays can hold up to 6 million discrete features, each of which contains millions of copies of one probe. (wikipedia.org)
  • Probe size: Early version of cDNA arrays had a probe length of about 200bp. (wikipedia.org)
  • Feb 2007) Probe composition: There are tiled and non-tiled DNA arrays. (wikipedia.org)
  • The hybridization signal intensities for each probe are used by specialized software to generate a log2ratio of test/normal for each probe on the array. (wikipedia.org)
  • Illumina
  • The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. (wikipedia.org)
  • organisms
  • Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. (wikipedia.org)
  • Since DNA is an informative macromolecule in terms of transmission from one generation to another, DNA sequencing is used in evolutionary biology to study how different organisms are related and how they evolved. (wikipedia.org)
  • RNAs
  • In the first step of the MICROB Enrich procedure, host-bacterial total RNA is incubated with an optimized mixture of capture oligonucleotides that bind to the mammalian 18S and 28S rRNAs and polyadenylated RNAs. (bio-medicine.org)
  • species
  • When the two species are mixed, the driver sequence is added in excess to tester. (wikipedia.org)
  • However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. (pubmedcentralcanada.ca)
  • Although many mammalian host species may be compatible with MICROB Enrich , only human, mouse and rat rRNA sequences were used for the design and optimization of the capture oligonucleotides. (bio-medicine.org)
  • tumors
  • The first report of CGH analysis was by Kallioniemi and colleagues in 1992 at the University of California, San Francisco, who utilised CGH in the analysis of solid tumors. (wikipedia.org)
  • commercially
  • However, in 1994 a review was published which described an easily understood protocol in detail and the image analysis software was made available commercially, which allowed CGH to be utilised all around the world. (wikipedia.org)
  • available
  • In order to assure the best possible match for features across different microarray platforms, we used mappings that matched each feature to genomic information available from the NCBI Entrez gene database. (nih.gov)
  • In addition, more recent publications have become available discussing methods for oligo design [ 25 - 30 ], due to the emergence of custom oligonucleotide arrays. (biomedcentral.com)
  • The motivation underlying the development of CGH stemmed from the fact that the available forms of cytogenetic analysis at the time (giemsa banding and FISH) were limited in their potential resolution by the microscopes necessary for interpretation of the results they provided. (wikipedia.org)
  • RNAtor RNAtor Android Application to calculate optimal parameters for popular tools and kits available for DNA sequencing projects. (wikipedia.org)
  • strains
  • We demonstrate here that marine cyanobacteria have a functionally active cyanase, the transcriptional regulation of which varies among strains and reflects the genomic context of cynS. (embl-heidelberg.de)
  • We have determined genome sequences of B strains [ 5 , 6 ] - REL606, which has been applied to the study of long-term experimental evolution, and BL21(DE3), which has been used as a cell-factory for overproducing recombinant proteins, biofuels, and a variety of bioproducts on an industrial scale. (biomedcentral.com)
  • transcriptome
  • In this work the transcriptome of S. cerevisiae was monitored throughout a wine fermentation, carried out in single culture or in a consortium with Hanseniaspora guilliermondii , this being the first time that this relevant yeast-yeast interaction is examined at a genomic scale. (biomedcentral.com)
  • Tiling arrays aid in transcriptome mapping as well as in discovering sites of DNA/protein interaction (ChIP-chip, DamID), of DNA methylation (MeDIP-chip) and of sensitivity to DNase (DNase Chip) and array CGH. (wikipedia.org)
  • Traditional methods of gene prediction for annotation of genomic sequences have had problems when used to map the transcriptome, such as not producing an accurate structure of the genes and also missing transcripts entirely. (wikipedia.org)
  • The first attempt at capturing a partial human transcriptome was published in 1991 and reported 609 mRNA sequences from the human brain. (wikipedia.org)
  • Amounts of individual transcripts were quantified using Northern blotting, nylon membrane arrays, and later Reverse Transcriptase quantitative PCR (RT-qPCR) methods, but these methods are laborious and can only capture a tiny subsection of a transcriptome. (wikipedia.org)
  • In addition, proteases recruited from remote sources like nearby tissues are ignored by these DNA based arrays, reiterating the need for protein based methods to confirm the presence and activity of functional enzymes when transcriptome analysis is performed. (wikipedia.org)
  • RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. (wikipedia.org)
  • organism
  • The budding yeast was the first eukaryote organism to have its genome sequenced [ 14 ], which paved the way for the development of robust advanced genetic tools that put this species at the forefront of '-omics' research. (biomedcentral.com)
  • synthesis
  • Every PCR primer pair was experimentally validated using Bio-Rad's iScript™ advanced cDNA synthesis kit and SsoAdvanced™ SYBR ® Green supermix. (bio-rad.com)
  • transcriptomic
  • By integrating results obtained in the transcriptomic analysis performed with physiological data our study provided, for the first time, an integrated view into the adaptive responses of S. cerevisiae to the challenging environment of mixed culture fermentation. (biomedcentral.com)
  • Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. (wikipedia.org)
  • Commercially
  • However, in 1994 a review was published which described an easily understood protocol in detail and the image analysis software was made available commercially, which allowed CGH to be utilised all around the world. (wikipedia.org)
  • generate
  • The hybridization signal intensities for each probe are used by specialized software to generate a log2ratio of test/normal for each probe on the array. (wikipedia.org)
  • Again, total RNA is extracted and used to generate cDNA for PCR amplification. (wikipedia.org)
  • Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and washing after hybridization. (wikipedia.org)
  • They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. (wikipedia.org)
  • 1970s
  • The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography. (wikipedia.org)
  • proteins
  • DNA sequencing is also the most efficient way to sequence RNA or proteins (via their open reading frames). (wikipedia.org)
  • Other proteins allow the identification of promoter regions, enhancers, repressors and silencing elements, insulators, boundary elements, and sequences that control DNA replication. (wikipedia.org)
  • Although such arrays are perfectly suited to study gene expression profiles, they have limited importance in ChIP experiments since most "interesting" proteins with respect to this technique bind in intergenic regions. (wikipedia.org)
  • In eukaryotes, transcription is performed by three types of RNA polymerases, each of which needs a special DNA sequence called the promoter and a set of DNA-binding proteins-transcription factors-to initiate the process. (wikipedia.org)
  • assay
  • Use the PrimePCR DNA contamination control assay to determine if genomic DNA (gDNA) is present in a sample at a level that may affect PCR results. (bio-rad.com)
  • chromosome
  • Earlier studies on chromosome 21 and 22 showed the power of tiling arrays for identifying transcription units. (wikipedia.org)
  • The aim of this technique is to quickly and efficiently compare two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole chromosomes or subchromosomal regions (a portion of a whole chromosome). (wikipedia.org)
  • contamination
  • QC-Chain QC-Chain is a package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. (wikipedia.org)
  • strand
  • With respect to a gene, the two strands may be labeled the "template strand," which serves as a blueprint for the production of an RNA transcript, and the "coding strand," which includes the DNA version of the transcript sequence. (wikipedia.org)
  • 1990s
  • Firstly, drug discovery in the last decades leading up to the 1990s had been limited due to the time and cost of running many chromatographic analyses in parallel on macroscopic equipment. (wikipedia.org)
  • copies
  • These arrays can hold up to 6 million discrete features, each of which contains millions of copies of one probe. (wikipedia.org)
  • Hybridization
  • The sequence signatures are deciphered by the parallel identification of four bases by hybridization to fluorescently labeled encoders (Figure 5). (wikipedia.org)
  • Each of the encoders has a unique label which is detected after hybridization by taking an image of the microbead array. (wikipedia.org)
  • This technique was originally developed for the evaluation of the differences between the chromosomal complements of solid tumor and normal tissue, and has an improved resoIution of 5-10 megabases compared to the more traditional cytogenetic analysis techniques of giemsa banding and fluorescence in situ hybridization (FISH) which are limited by the resolution of the microscope utilized. (wikipedia.org)
  • The most important elements are, among others, hybridization ovens, chip scanners, and software packages for subsequent numerical analysis of the raw data. (wikipedia.org)
  • Pathway Analysis
  • used Ingenuity Pathway Analysis (IPA) software that associated exRNAs found in human blood microvesicles with pathways involved in blood cell differentiation, metabolism, and immune function. (wikipedia.org)
  • fluorescence
  • It was concluded that the fluorescence ratios obtained were accurate and that differences between genomic DNA from different cell types were detectable, and therefore that CGH was a highly useful cytogenetic analysis tool. (wikipedia.org)
  • Following the development of fluorescence-based sequencing methods with a DNA sequencer, DNA sequencing has become easier and orders of magnitude faster. (wikipedia.org)
  • specific
  • Virtual karyotype is the digital information reflecting a karyotype, resulting from the analysis of short sequences of DNA from specific loci all over the genome, which are isolated and enumerated. (wikipedia.org)
  • parallel
  • Fluorescent imaging captures the signal from all of the beads, while affixed to a 2-dimensional surface, so DNA sequences are determined from all the beads in parallel. (wikipedia.org)
  • different
  • Array-based karyotyping can be done with several different platforms, both laboratory-developed and commercial. (wikipedia.org)
  • The authors painted a series of individual human chromosomes from a DNA library with two different fluorophores in different proportions to test the technique, and also applied CGH to genomic DNA from patients affected with either Downs syndrome or T-cell prolymphocytic leukemia as well as cells of a renal papillary carcinoma cell line. (wikipedia.org)
  • targets
  • For example, an analysis of the miRNAs highly conserved in vertebrates shows that each has, on average, roughly 400 conserved targets. (wikipedia.org)