• 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)
  • Current cancer research makes use primarily of DNA microarrays in which an arrayed series of microscopic spots of pre-defined DNA oligonucleotides known as probes are covalently attached to a solid surface such as glass, forming what is known as a gene chip. (wikipedia.org)
  • DNA microarrays evolved from Southern blotting which allows for detection of a specific DNA sequence in a sample of DNA. (wikipedia.org)
  • Microarrays are a significant advance because of their small size and are therefore useful when one wants to survey a large number of genes quickly or when the study sample is small. (medscape.com)
  • Microarrays may be used to assay gene expression within a single sample or to compare gene expression in 2 different cell types or tissue samples, such as in healthy versus diseased tissue. (medscape.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)
  • The 2 most common microarray technologies in use are the oligonucleotide microarrays and the robotically spotted complementary DNA (cDNA) microarrays. (medscape.com)
  • Oligonucleotide microarrays are manufactured by Affymetrix (Santa Clara, Calif) using photolithographic techniques. (medscape.com)
  • Microarrays, by making use of the sequence resources created in genomic projects, are a powerful technology capable of measuring the expression levels of thousands of genes simultaneously and have dramatically expedited comprehensive understanding of gene expression profiles for disease development. (biomedcentral.com)
  • Stu Borman, Chemical and Engineering News, Dec. 16, 2002 lists as highlights of 2002 http://pubs.acs.org/cen/coverstory/8050/8050chemhighlights5.html with references to the literature on polysaccharide and glycoconjugate microarrays, monosaccharide chips, natural and synthetic oligosaccharide arrays, and synthetic oligosaccharides in microtiter plate format. (genomicglossaries.com)
  • Affymetrix GeneChips are commercially available microarrays appropriate for transcript profiling of samples from a number of species. (upenn.edu)
  • Target pools can be radiolabeled for hybridization to membrane arrays or be directly or indirectly (with or without IVT amplification) labeled with fluorescent dyes for competitive hybridization to glass microarrays. (upenn.edu)
  • Some of those technologies were indeed available - such as microarrays for Arabidopsis and human and mouse cDNAs - but were scattered over different laboratories with relatively little coordination. (genomyx.ch)
  • Arrayit Pathways™ Focused Human Genome Microarrays enable targeted gene expression analysis of every major cellular pathway in the human body. (arrayit.com)
  • Pathways™ Microarrays offer the highest sensitivity and specificity of any product on the market, empowered by long-mer oligonucleotides, proprietary attachment and surface chemistry, and a unique one gene-one spot™ design. (arrayit.com)
  • The use of advanced bioinformatics, ultra-pure oligonucleotides, superior surface chemistry and advanced microarray cleanroom manufacturing facilities guarantees that Pathways™ Microarrays outperform the highest industry standards. (arrayit.com)
  • These microarrays are designed using the complete, fully annotated human genome sequence using sophisticated one spot-one gene™ informatics, useding highest gene content available. (arrayit.com)
  • All our microarrays offer quality and performance that cannot be obtained from any other microarray, PCR or next generation sequencing approach. (arrayit.com)
  • The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
  • The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.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)
  • Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells. (takarabio.com)
  • We performed Next Generation Sequencing (Illumina Next Seq) of 115 SNPs in a discovery cohort of 120 metformin users and conducted a systematic literature review. (bvsalud.org)
  • 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 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)
  • More than 700 miRs have been identified and registered in humans, with each individual miR predicted to target multiple genes based on the seed sequence matches in their 3'-untranslated regions (UTRs) [ 6 ]. (biomedcentral.com)
  • We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
  • Using Affymetrix Gene Chip analysis, we have identified genes linked to regenerative success downstream of BMP signalling, including the BMP inhibitor Gremlin and the stress protein Hsp60 ( no blastema in zebrafish). (biomedcentral.com)
  • Gene Ontology analysis showed that genes involved in embryonic development and growth are significantly over-represented in regenerating early hindlimb buds and that successful regeneration in the Xenopus hindlimb correlates with the induction of stress response pathways. (biomedcentral.com)
  • First, large-scale full-length cDNA sequencing efforts have made it clear that most if not all genes are transcribed in different isoforms owing both to splice variation, alternative termination, and alternative TSSs [ 9 ]. (biomedcentral.com)
  • 687 genes differentiated tumor samples before and after treatment, among which 310 genes did not show the same differential expression in the placebo group or normal samples. (karger.com)
  • Sixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. (biomedcentral.com)
  • Twenty-three genes, which were differentially expressed between adjacent normal and tumor samples, were selected and analyzed using 24 paired lung adenocarcinoma samples by Q-RT-PCR using two internal controls, DDX5 and GAPDH . (biomedcentral.com)
  • An appropriate internal control for Q-RT-PCR should be expressed stably across all data samples and if this is true, measurement of genes relative to the internal control will reflect the real gene expression. (biomedcentral.com)
  • TFs are known as master switch in plant stress response, and genetic transformation of the genes encoding TFs has been suggested as a possible approach for engineering stress tolerance as manipulation of a single TF can alter expression of a wide array of target genes [ 7 ]. (biomedcentral.com)
  • Genome-wide analysis of gene expression provides insight into the transcriptional state of a cell or tissue sample, measuring RNA levels for thousands of genes in parallel. (biomedcentral.com)
  • A panel of 11 genes selected according to microarray analysis were validated and tested further in 11 cancer cell lines, resulting in 4 genes, CXCR4, CDK6, USP15 and CDH1. (iiarjournals.org)
  • The majority of the top 15 differentially expressed genes for each tissue were known to either be expressed in a tissue-specific manner or relate to specific functions of that tissue. (cambridge.org)
  • Gene ontology analysis of the differentially expressed genes revealed the expected differences in gene expression profiles between the two tissues. (cambridge.org)
  • 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)
  • As functional annotations accumulate, detailed and in-depth studies of specific genes and their products can be placed into a genomic context to reveal the molecular systems in which biological processes occur. (upenn.edu)
  • system for DNA replication that allows a "target" DNA sequence to be In medical science, PCR is used for the detection of infectious organisms and the detection of mutation in various genes. (nervegarden.com)
  • The present study is usually a cross-sectional analysis aimed to evaluate the significance of the presence of SE genes, defined as em DRB1*01 /em or em DRB1*04 /em , in relation to anti-CCP antibodies, antikeratin antibody (AKA) and RF in individuals who developed RA. (exposed-skin-care.net)
  • Using such probes, one can obtain a fingerprint of the gene expression activity in a macroscopic sample. (lu.se)
  • The array consisted of exon probes and thermodynamically balanced junction probes. (biomedcentral.com)
  • Suboptimal probes were tagged and considered in the final analysis. (biomedcentral.com)
  • These arrays contain oligonucleotide probes that span exon-exon junctions, and probes positioned within exons to determine individual exon levels and overall transcript expression. (biomedcentral.com)
  • One of the drawbacks of micro-array expression measurements has been that the expression measured by hybridization at individual probes is often a combination of expression of different transcript isoforms that may be associated with different promoters and may be regulated in different ways [ 10 ]. (biomedcentral.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)
  • To compare experiments that are performed on these different platforms, array probes and sequence tags need to be linked. (biomedcentral.com)
  • Array probes are produced by polymerase chain reaction (PCR) amplification of selected cDNAs or designed on the basis of cDNA or gene sequence information. (biomedcentral.com)
  • Cross-referencing array probes allows comparison of studies carried out using different technologies, and facilitates validation of gene expression. (biomedcentral.com)
  • In addition, the database can be used to annotate array probes with reference sequences and updated gene descriptions from UniGene. (biomedcentral.com)
  • Transcript profiling can be open-ended, using methods that do not rely on previous knowledge of gene sequences, or closed to a defined set of probes for known RNAs. (upenn.edu)
  • Like northern blot probes, microarray probes have a known (or knowable) sequence and concentration, but are immobilized in an array on a surface substrate at defined locations. (upenn.edu)
  • Probes may be PCR products from cDNA clones, long oligomers that are pre-synthesized and then printed as an array, or short oligomers synthesized directly on the array substrate. (upenn.edu)
  • Depending on the array type, eleven to twenty independent probes are chosen for each unique UniGene accession and synthesized as 25 nucleotide oligomers. (upenn.edu)
  • New version GeneChips are now available with 11 micron features and over one million probes per array. (upenn.edu)
  • An optimised reverse transcriptase for production of full-length cDNA from as little as 100pg of total RNA/low abundance RNA. (biosearchtech.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)
  • They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. (genomicglossaries.com)
  • Probe collections were at first PCR amplification products from cDNA templates, but now can include PCR products from BACs, 60-70mer oligonucleotides, or shorter derivitized oligomers that specifically attach to coated surfaces. (upenn.edu)
  • Here are the latest publications comparing PicoPLEX technology to other single-cell whole-genome amplification technologies, and using PicoPLEX technology to uncover insights from CTCs, single cells from FFPE tumor samples, and samples relevant to preimplantation genetic testing. (takarabio.com)
  • The PicoPLEX DNA-seq Kit did not require a separate library preparation step as the kit performs whole genome amplification (WGA) and library construction simultaneously, resulting "in a sequencing-ready library, using a single-tube reaction. (takarabio.com)
  • The study concluded that "PicoPLEX showed the best performance in the quality of sequencing data, uniformity of read depth, amplification reproducibility and fidelity," and "recommended [PicoPLEX] for CNV calling on Ion Proton platform. (takarabio.com)
  • DNA was first extracted from microdissected FFPE tissues, and then the PicoPLEX WGA Kit was used to perform whole genome amplification. (takarabio.com)
  • Indeed, if the sequence of interest is present in the DNA extract, it is possible to selectively replicate it (we speak of amplification) in very large numbers. (intechopen.com)
  • Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)
  • These kits generate high yields of genomic DNA, total cellular DNA or total nucleic acids (TNA) in under 60 minutes. (biosearchtech.com)
  • Since November 2003, Dr. Keith Harshman has been the Coordinator of the Lausanne Genomic Technologies Facility (GTF), providing customers with State of the Art technologies to detect and measure quantitative and qualitative variations in nucleic acids. (genomyx.ch)
  • When performing high-throughput sequencing on the other hand, there is no need for such a priori assumptions: whereas a micro-array tells you whether a complementary sequence to a given pre-designed oligo is present in your sample, massive sequencing also reveals the presence of nucleic acids that were not sought after. (genomyx.ch)
  • Digital PCR (dPCR) can be used to directly quantify and clonally amplify nucleic acids including DNA, cDNA, mRNA or microRNA. (gene-quantification.de)
  • However, compared to other flaviviruses, USUV has received less research attention and there is therefore limited access to whole-genome sequences and also to in-depth phylogenetic and phylodynamic analyses. (frontiersin.org)
  • This paper compared the performance of the PicoPLEX DNA-seq Kit , the DOPlify WGA Kit, the REPLI-g Single Cell Kit, and the Ampli1 WGA Kit for aneuploidy screening and copy number analysis using shallow whole genome sequencing, starting from one, three, or five cells isolated from the Loucy cell line. (takarabio.com)
  • Cells were whole-genome amplified, followed by PCR-free library preparation and Illumina sequencing. (takarabio.com)
  • With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
  • During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.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)
  • This allows for the simultaneous preparation of multiple cells by pooling them after cDNA synthesis, increasing the throughput and efficiency of scRNA-seq library preparation. (molcells.org)
  • Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
  • Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)
  • Three specific modifications, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and N1-methylguanosine (m1G), are abundant in eukaryotic tRNAs and are particularly problematic for reverse transcriptases (RTs) by causing cDNA synthesis to stop or misincorporate. (cdc.gov)
  • 2003 ). The NHGRI has categorized new sequencing approaches into those that offer near-term and revolutionary benefits with a 100-fold cost reduction per base pair (bp) within the next five years. (springer.com)
  • This review will focus on the contribution of high-throughput genomic and proteomic approaches to the study of fibrogenesis and fibrosis progression, concentrating on the most prevalent human chronic liver diseases and findings from animal models in liver tissue, isolated liver cells, cell lines and serum. (biomedcentral.com)
  • There are several advantages that deep-sequencing approaches to gene expression analysis offer over standard micro-array approaches. (biomedcentral.com)
  • Other advantages of deep sequencing approaches are that they avoid the cross-hybridization problem that micro-arrays have [ 11 ], and that they provide a larger dynamic range. (biomedcentral.com)
  • With emphasis on MinION Nanopore sequencing, cDNA-direct and target-enrichment (amplicon-based) sequencing approaches were validated in parallel. (frontiersin.org)
  • There are also ways to combine both approaches by starting with an open-ended functional enrichment of transcribed sequences and using them to create probe collections for further profiling before determining their identities. (upenn.edu)
  • The study of biological complexity is a new frontier that requires high-throughput molecular technology, high speed computer memory, new approaches to data analysis, and the integration of interdisciplinary skills. (intechopen.com)
  • Messenger RNA (mRNA) from the sample of interest can serve as a template for producing complementary DNA (cDNA) in the presence of a reverse transcriptase enzyme. (medscape.com)
  • Expression levels of miR that showed significant differences between the 2 ESCC and Het-1A cells based on the comprehensive analysis were analyzed by the quantitative reverse transcriptase (RT)-PCR method. (biomedcentral.com)
  • Array-based technologies measure hybridization signal intensities in one or two channels for each array feature or probe, resulting in absolute or relative information about the expression levels of the corresponding transcripts in the samples. (biomedcentral.com)
  • Hybridization conditions and probe compositions are such that the target sequence should hybridize to the perfect match but not the mismatch probe. (upenn.edu)
  • Single-stranded target DNAs have been efficiently used in the studies of micro-array hybridization (4-7) and direct sequencing of DNA (1,8). (nervegarden.com)
  • Paired-end, strand specific sequencing for total RNA was performed on Illumina HiSeq 2500 with 100 bp read lengths. (nih.gov)
  • The amplified DNA underwent exome capturing, followed by sequencing on both Illumina HiSeq® 2000 and Thermo Fisher Ion Proton platforms. (takarabio.com)
  • We used the Affymetrix Human Genome U133 A and B GeneChip sets [ 16 ] to establish the gene expression in normal kidney tissues and distinct types of renal cell tumours. (biomedcentral.com)
  • Use of the Affymetrix Human GeneChip array and genomic. (cambridge.org)
  • However, no sheep-specific Affymetrix GeneChip is currently available and the bovine array is fairly limited in its coverage and annotation. (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)
  • Affymetrix maintains databases of target and probe sequences, annotations, and documentation that are readily available to GeneChip users (see www.affymetrix.com ). (upenn.edu)
  • DNA labeled with fluorophores (target) is prepared from a sample such as a tumor biopsy and is hybridized to the complementary DNA (cDNA) sequences on the gene chip. (wikipedia.org)
  • third oligonucleotide bearing fluorescent moieties is required and is complementary A new method for replicating DNA in the lab, named COMPAS-PCR, short for COMplementary Primer Asymmetric PCR, has been developed by scientists at the Norwegian Institute for Water Research. (nervegarden.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)
  • Rapid and comprehensive analysis of putative proteinous allergens ( allergenome ) by applying such a proteomic strategy … With allergenomics, we can not only detect and assign the putative allergens (proteins specifically interacting with IgE antibodies in a patient's blood) in a short time, but also analyze the quantitative and qualitative change of the antigens, depending on the surroundings and environmental conditions of an allergenic causative. (genomicglossaries.com)
  • Current genomic and proteomic research provides many candidate biomarkers, but independent validation of these biomarkers is lacking, and reproducibility is still a key concern. (biomedcentral.com)
  • A special focus is lying on the integrative analysis of multi level biomarkers, e.g. microRNA - mRNA, integrative analysis of genomic, proteomic, metabolomic and phenotypic markers. (gene-quantification.de)
  • C. Peterson, M. Ringne´r / Artificial Intelligence in Medicine 28 (2003) 59-74 structure and function, cellular metabolism, development of cells and tissues, and response of organisms to their environments. (lu.se)
  • Then, functional analyses, including cellular proliferation, apoptosis and Matrigel invasion and the wound healing assay, for the specific miR were conducted. (biomedcentral.com)
  • The term "oncotarget" encompasses all molecules, pathways, cellular functions, cell types, and even tissues that can be viewed as targets relevant to cancer as well as other diseases. (oncotarget.com)
  • gene in a series of tissue types, throughout stages of development or cellular However, asymmetric PCR is the most cost effective method for ssDNA production. (nervegarden.com)
  • Nonetheless, the recent and continuous development of new single-cell RNA sequencing (scRNA-seq) toolkits has enabled researchers to compare transcriptomes at a single-cell resolution, thus facilitating the analysis of individual cellular features and a deeper understanding of cellular functions. (molcells.org)
  • Author Manuscript class of cellular RNA for which the standard sequencing methods cannot yet be applied efficiently and quantitatively, although attempts have been made (e.g. ref 2). (cdc.gov)
  • The primary service of microbial arrays has been characterization of agents propagated to high titer in vitro ( 6 ). (cdc.gov)
  • These include cDNA clone libraries, Affymetrix GeneChips, and oligonucleotide sets for human, mouse and rat (Table 1 ). (biomedcentral.com)
  • Microarray analysis was performed according to Affymetrix protocols (Santa Clara, CA USA). (iiarjournals.org)
  • To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), and third-generation (MinION Nanopore) sequencing platforms for USUV. (frontiersin.org)
  • Sanger sequencing was performed on the amplified DNA to confirm the results obtained from dPCR KRAS mutation analysis. (takarabio.com)
  • However, it is not sufficient when larger numbers of known pathogens must be considered, when new but related pathogens are anticipated, or when sequence divergence might impair binding of PCR primers. (cdc.gov)
  • The absence of DNA contamination in RNA samples was confirmed by PCR of GAPDH with primers specific to genomic DNA. (biomedcentral.com)
  • Primer Design Design three adjacent primers from your sequence (priming outwards from the sequence). (nervegarden.com)
  • primers that bind specifically to the known sequence and point in opposite http://www.bio.davidson.edu/courses/genomics/method/NestedPCR.html). (nervegarden.com)
  • Within the known sequence, TAIL-PCR uses a nested pair of primers with differing annealing temperatures. (nervegarden.com)
  • a pair of PCRs run in series each with a pair of primers flanking the same expression levels when defining tissue-restricted gene expression patterns. (nervegarden.com)
  • Levels of gene expression are measured using a preparation of fluorescently labeled tissue RNA (copies of DNA), together with reference RNA labeled with a different fluorochrome, hybridized onto the slides. (lu.se)
  • This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. (medscape.com)
  • EDN3 mRNA expression was assessed by Northern blotting in normal human tissues (n = 9) as well as in matched pairs of normal and tumourous tissues from breast specimens (n = 50). (biomedcentral.com)
  • We observed similar metabolic alterations that correlated with MUC16 expression in primary tumor tissue specimens from human pancreatic adenocarcinoma cancer patients. (oncotarget.com)
  • Results: Only CXCR4 mRNA levels in gastric cancer tissues were correlated with docetaxel sensitivity (R 2 =0.23, p=0.019) and significantly higher in resistant specimens (p=0.038). (iiarjournals.org)
  • Automation-compatible products for high-quality RNA extraction and purification from a range of clinical samples, including upper respiratory specimens. (biosearchtech.com)
  • Digital PCR Improves Mutation Analysis in Pancreas Fine Needle Aspiration Biopsy Specimens. (takarabio.com)
  • The field of functional genomics seeks to annotate genomic sequence with assignments of gene and regulatory element identities and locations, RNA variants and expression levels, and protein variants, abundance and interactions. (upenn.edu)
  • Previously, a probe-selection method based on hybridisation of genomic DNA (gDNA) was developed, which enables GeneChips to be used for species that they were not designed for. (cambridge.org)
  • The unique pattern of gene expression for a given cell or tissue is referred to as its molecular signature. (wikipedia.org)
  • Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. (genomicglossaries.com)
  • And I must add that the transition to high-throughput sequencing was fairly smooth, because much of the molecular biology and data analysis is fairly similar to the experimental work our team had been doing thus far. (genomyx.ch)
  • Biomolecular Detection and Quantification (BDQ) is an open access, peer-reviewed international journal dedicated to championing excellence in molecular study design, measurement, data analysis and reporting. (gene-quantification.de)
  • A session about the discovery, identification and validation of molecular biomarkers: diagnostic, prognostic or therapeutic markers on DNA, RNA, microRNA or small RNA, metabolome and proteome level (e.g. disease markers, cancer or stem-cells markers, tissue specific markers, differentiation markers, methylation markers). (gene-quantification.de)
  • Focus is on micro-genomics, the application of molecular methods to detect biomarkers in a minimal amount of tissue or matrix. (gene-quantification.de)
  • Loss of METTL16 and SNRNP27K orthologs, or a single SNRNP27K methionine residue, was associated with a preference for +4 U. These findings are consistent with splicing analyses of mutants defective in either METTL16 or SNRNP27K orthologs and models derived from spliceosome structures, demonstrating that inter-species association mapping is a powerful orthogonal approach to molecular studies. (bvsalud.org)
  • To address this and to also study the oncogenic potential of unregulated function of dominant regulators of epithelial homeostasis noted above, we developed Multi-Functional Human Tissue Genetics noted above which, when combined with skin tissue regeneration on immune deficient mice, has permitted the molecular reconstruction of events sufficient to trigger human cancer. (stanford.edu)
  • Between 17,000,000 and 57,000,000 reads were obtained for each sample, and ~75-90% of reads were successfully mapped to the genome for each sample. (nih.gov)
  • The 'CAGE tags' thus obtained can then be sequenced and mapped to the genome. (biomedcentral.com)
  • Dr. Harshman, I would not be surprised at all if you were to tell me that you have been interested in genomics and sequencing since you were a small boy, like those whizz-kids who can play the violin before they can properly walk. (genomyx.ch)
  • My fascination for genomics and genomic-related issues came later - somewhere around the early nineties - when I was employed at Myriad Genetics Inc , a small Biotech Company in Salt Lake City, Utah. (genomyx.ch)
  • SAGE results in quantitative information connected to 10-14 base-pair (bp) sequence tags derived from the 3' ends of transcripts. (biomedcentral.com)
  • More than 20 000 transcripts were detected in triplicate ovine skeletal muscle and liver samples, which is more than would be possible using the commercially available sheep-specific microarray. (cambridge.org)
  • Using ESCC tumor samples and paired surrounding non-cancerous tissue obtained endoscopically, the association with histopathological differentiation was examined with quantitative RT-PCR. (biomedcentral.com)
  • EDN3 promoter methylation was analysed by methylation-specific PCR in breast cell lines (n = 6) before and after demethylating treatment, normal breast tissues (n = 17) and primary breast carcinomas (n = 128). (biomedcentral.com)
  • Furthermore, EDN3 promoter hypermethylation was detected in 70% of primary breast carcinomas with significant association to loss of EDN3 mRNA expression ( P = 0.005), whilst normal matched breast tissues revealed no EDN3 promoter methylation. (biomedcentral.com)
  • Epigenetic control of gene expression lasts through multiple cell divisions without alterations in primary DNA sequence and can occur via mechanisms that include histone modification and DNA methylation. (stanford.edu)
  • Grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses ( e.g. , homology-based prediction of structure or function). (biomedcentral.com)
  • This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. (biomedcentral.com)
  • 80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. (mdpi.com)
  • With the advent of deep sequencing technologies it has now become practical to sequence CAGE tag libraries to much greater depth, providing millions of tags from each biological sample. (biomedcentral.com)
  • These new models, which we term Multi-Functional Human Tissue Genetics, allow up to 10 alleles or more to be altered simultaneously, permitting genetic experiments with an unprecedented degree of rapidity and complexity. (stanford.edu)
  • For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
  • Unlike such genetic changes, epigenetic changes, which do not alter genome sequence, can result in three possible outcomes: passive dilution, active repair through negative feedback, or active maintenance through positive feedback. (nature.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)
  • Genetic studies have exhibited multiple HLA- em DRB1 /em alleles encoding a conserved sequence at amino acid positions 70C74 are associated with susceptibility and severity of RA. (exposed-skin-care.net)
  • The level of fluorescence at a particular spot provides quantitative information about the expression of the particular gene corresponding to the spotted cDNA sequence. (wikipedia.org)
  • 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)
  • In particular, we have developed rigorous procedures for normalizing the data, a quantitative noise model, and a Bayesian procedure that uses this noise model to join sequence reads into clusters that follow a common expression profile across samples. (biomedcentral.com)
  • Separate analysis algorithms are used to make a detected/not detected call and assign a quantitative signal for each targeted gene. (upenn.edu)
  • We applied two strategies to eliminate or substantially reduce the obstacles of tRNA modification and structure for efficient and quantitative tRNA sequencing ( Fig. 1a ). (cdc.gov)
  • Because no unique gene nomenclature or sequence identifier is used for all platforms, a database linking the different identifiers belonging to one gene and its orthologs is required. (biomedcentral.com)
  • Our experimental focus is on the mammalian setting using multiomics, informatics, mouse genetics, human genetics, single cell studies, and new human tissue platforms. (stanford.edu)
  • Because, no matter how many answers micro-array technology can provide, you have to make assumptions - to some extend you have to know what you are searching for within your experimental set-up - in order to represent a particular nucleic acid sequence with an oligonucleotide on a gene chip. (genomyx.ch)
  • The precise splicing of Vv-circSIZ1 does not depend on its mature exon sequence or internal intron sequences, but on the AG/GT splicing signal sites and branch site of the flanking introns. (bvsalud.org)
  • We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
  • Histological methods rely on chemical staining of tissues with pigments such as haematoxylin and eosin and microscopy-based visualization by a pathologist. (wikipedia.org)
  • Analysis of nasopharyngeal aspirates, blood, urine, and tissue from persons with various infectious diseases confirmed the presence of viruses and bacteria identified by other methods, and implicated Plasmodium falciparum in an unexplained fatal case of hemorrhagic feverlike disease during the Marburg hemorrhagic fever outbreak in Angola in 2004-2005. (cdc.gov)
  • These large-scale high-throughput analytical methods have been applied to the identification of differential splicing events in cancer tissues [ 8 ]. (biomedcentral.com)
  • Here we present a set of rigorous methods for normalization, quantification of noise, and co-expression analysis of deep sequencing data. (biomedcentral.com)
  • Using these methods on 122 cap analysis of gene expression (CAGE) samples of transcription start sites, we construct genome-wide 'promoteromes' in human and mouse consisting of a three-tiered hierarchy of transcription start sites, transcription start clusters, and transcription start regions. (biomedcentral.com)
  • However, early methods processed cell samples in bulk, and therefore the unique transcriptomic patterns of individual cells would be lost due to data averaging. (molcells.org)
  • Despite these advantages, microbial arrays have not been widely used with clinical materials because of limited sensitivity. (cdc.gov)
  • 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)
  • Rare mutations in genome sequence that result from failed DNA repair are transmitted across generations through DNA replication during each cell division. (nature.com)
  • Five SNPs were confirmed in a combined analysis of both replication cohorts but showed different association patterns in subgroup analyses. (bvsalud.org)
  • Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
  • Computer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequence variants. (biomedcentral.com)
  • Since the introduction of RNA sequencing (RNA-seq) as a high-throughput mRNA expression analysis tool, this procedure has been increasingly implemented to identify cell-level transcriptome changes in a myriad of model systems. (molcells.org)
  • In contrast, because deep sequencing allows measurement of expression along the entire transcript the expression of individual transcript isoforms can, in principle, be inferred. (biomedcentral.com)
  • Our mag kits are a high-throughput and cost-effective DNA isolation method suitable for PCR, sequencing and genotyping. (biosearchtech.com)
  • The study found that PicoPLEX DNA-seq libraries "detected 100% of the CNVs that were also detected in the sequenced bulk sample. (takarabio.com)
  • NGS libraries were constructed for sequencing on the Ion Proton platform. (takarabio.com)
  • PtrABF had a complete open reading frame of 1347 bp, encoding a 448 amino acid peptide, and shared high sequence identities with ABFs from other plants. (biomedcentral.com)
  • These developed HT-NGS strategies addressed our anticipated future needs of throughput sequncing and cost, in a way which enabled its potential multitude of current and future applications in mammalian genomic research. (springer.com)
  • With the advent of ultra high-throughput sequencing technologies, increasingly researchers are turning to deep sequencing for gene expression studies. (biomedcentral.com)
  • In recent years several technologies have become available that allow DNA sequencing at very high throughput - for example, 454 and Solexa. (biomedcentral.com)
  • Although these technologies have originally been used for genomic sequencing, more recently researchers have turned to using these 'deep sequencing' or '(ultra-)high throughput' technologies for a number of other applications. (biomedcentral.com)
  • Unfortunately, such devices do not allow for high throughput analysis due to the manual effort involved in operating the valving mechanisms. (justia.com)
  • Most of the questions that were being answered by using micro-arrays are now being addressed, mostly in a more comprehensive manner, with high-throughput sequencing. (genomyx.ch)
  • High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)
  • This process is repeated to build specific oligonucleotide sequences. (medscape.com)
  • In general, a sequence-specific identifier (GenBank accession number) serves as a reference to the array probe sequence. (biomedcentral.com)
  • A set of two priming oligonucleotides and a third allele-specific primer were used to identify heterozygotes for a G to A mutation at nucleotide 10,708 in the apolipoprotein B (apo B) gene. (nervegarden.com)
  • CircSIZ1 is species-specific, and genomic circSIZ1-forming region of seven tested species could be backspliced in Nicotiana benthamiana, but not in Arabidopsis. (bvsalud.org)
  • Probe sequences are chosen from the public UniGene databases and synthesized by photolithography directly on the array surface. (upenn.edu)