Protein genomic or cdna oligonucleotide array sequence analysis. Medical search. Frequent questions

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)
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. (nih.gov)
The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. (nih.gov)
These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
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)
With 35,000 genes and hundreds of thousands of protein states to identify, correlate, and understand, it no longer suffices to rely on studies of one gene, gene product, or process at a time. (genomicglossaries.com)
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)
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)
Interestingly, several alkali induced genes/proteins can provide a cross protective overlap to other types of stresses. (essex.ac.uk)
Supervised analysis of kinase genes revealed a high-level FLT3 expression in a subset of cases without molecular rearrangements. (aacrjournals.org)
Genomic profiling also identifies genes associated with poor outcome in cases without molecular aberrations and specific genes that may be new therapeutic targets in adult ALL. (aacrjournals.org)
Iron regulatory proteins (IRPs) 1 and 2 post-transcriptionally control mammalian iron homeostasis by binding to iron-responsive elements (IREs), conserved RNA stem-loop structures located in the 5'- or 3'- untranslated regions of genes involved in iron metabolism (e.g. (uni-wuerzburg.de)
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)
Gene ontology analysis of the differentially expressed genes revealed the expected differences in gene expression profiles between the two tissues. (cambridge.org)
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)
The original designs of most of the PCR primers used for the analysis of 16S rRNA genes were based on known sequences deposited in public databases. (frontiersin.org)
For example, a complete 16S rRNA gene sequence can be obtained by analyzing the sequences of genomes or large genome fragments, providing taxonomic information along with information on other functional genes. (frontiersin.org)
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)
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)
In addition, steady-state mRNA levels of nine stress-responsive genes coding for either functional or regulatory proteins were induced to higher levels in the transgenic lines with or without drought stress. (biomedcentral.com)
Products of the former group function directly in protecting cells against damage derived from stresses and sustaining cell viability, and the latter is composed of regulatory proteins, such as transcription factors (TFs), protein kinases and protein phosphatases, that are responsible for transducing stress signaling and regulating expression of stress-responsive genes [ 5 ]. (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)
The selected pathways were used to design panels of real-time PCR primers tailored for the top-ranked genes for differential gene expression analysis. (bio-rad.com)
Reference genes are used in relative gene expression analysis to normalize for variation in the amount of input messenger RNA (mRNA) among samples. (bio-rad.com)
Differentially regulated genes were validated at the level of gene and protein expression, with genes identified as estrogen-regulated in human confirmed as estrogen-dependent in young estrogen depleted mice in vivo . (biomedcentral.com)
Moreover, direct estrogen regulation is demonstrated for three array-identified genes, Sele , Lypd3 and Arg1 , in mouse cells in vitro . (biomedcentral.com)
CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. (frontiersin.org)
Further analysis revealed that a lower AR occupancy was accompanied by a reduction in FoxA1 binding at regulatory regions of AR-dependent genes. (oncotarget.com)
Both p53 and AR are transcription factors and can affect the expression of a broad array of genes. (oncotarget.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)
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)
Two of the most common uses of the DNA microarrays are genetic analysis and the analysis of gene expression. (ddw-online.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)
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)
Gene expression profiles from 128 adult patients with newly diagnosed ALL were characterized using high-density oligonucleotide microarrays. (aacrjournals.org)
The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. (uni-wuerzburg.de)
2006). The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. (uni-wuerzburg.de)
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)
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)

As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)
Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells. (takarabio.com)
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)
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)
Determination of DNA methylation variation across the whole genome via bisulfite sequencing or sequencing of fragments generated by methylation restriction polymorphisms, purification of methylated fragments by antibody affinity, or methyltransferase trapping. (elimbio.com)

Every PCR primer pair was experimentally validated using Bio-Rad's iScript™ advanced cDNA synthesis kit and SsoAdvanced™ SYBR ® Green supermix. (bio-rad.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)
strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. (frontiersin.org)
Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. (frontiersin.org)

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)
Year 2011 is celebrated as the 10th anniversary since the human genome was first sequenced ( www.nature.com/natureconferences/hg10years/index.html ). (springer.com)

Treatment of alkali-adapted cells with the protein synthesis inhibitor chloramphenicol has revealed that the AlTR is at least partially protein-dependent. (essex.ac.uk)
To obtain a better understanding of metabolically active microbial communities, we tested a molecular ecological approach using poly(A) tailing of environmental 16S rRNA, followed by full-length complementary DNA (cDNA) synthesis and sequencing to eliminate potential biases caused by mismatching of polymerase chain reaction (PCR) primer sequences. (frontiersin.org)
A Real Time Analysis program actively interprets the raw data to determine each base being incorporated as the sequence-by-synthesis occurs. (elimbio.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)
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)
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)

Considering the current limitations of NGS technology, full-length 16S rRNA gene sequences are better suited to downstream analytical methods such as fluorescence in situ hybridization. (frontiersin.org)

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)
The sequences obtained using the poly(A) tailing method were compared statistically and phylogenetically with those obtained using conventional reverse transcription-PCR (RT-PCR) with published domain-specific primers. (frontiersin.org)
Numerous studies on natural microbial communities from a variety of environments have been undertaken using 16S rRNA gene sequencing mediated by polymerase chain reaction (PCR) with oligonucleotide primers. (frontiersin.org)

Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (ind.in)
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)
Sanger sequencing was performed on the amplified DNA to confirm the results obtained from dPCR KRAS mutation analysis. (takarabio.com)

Researchers are still confronted with challenging questions after completing the expression profiling and these include how to validate and standardize the data processing using proper statistical analysis. (biomedcentral.com)

Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. (nih.gov)
Iron is part of hemoproteins, iron-sulfur (Fe-S) proteins, and other proteins with functional groups that require iron as a cofactor. (uni-wuerzburg.de)
Then, functional analyses, including cellular proliferation, apoptosis and Matrigel invasion and the wound healing assay, for the specific miR were conducted. (biomedcentral.com)

The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip, but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. (uni-wuerzburg.de)

Genetic analysis includes procedures for genotyping, SNP (single nucleotide polymorphism) detection, strain identification and various other procedures. (ddw-online.com)
[ 7 ] They consist of a glass surface onto which oligonucleotides consisting of 25 bases are built a single nucleotide at a time. (medscape.com)
The massive efforts to systematically find and catalog single nucleotide polymorphisms (SNPs) bear witness to the conviction that small genomic changes may provide clues to the origins of such things as heart problems, obesity, and pharmacologic responses. (the-scientist.com)

However, no sheep-specific Affymetrix GeneChip is currently available and the bovine array is fairly limited in its coverage and annotation. (cambridge.org)
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)

Bcl2/adenovirus EIB 19kD-interacting protein 3 (BNIP3) is a cell death factor that is a member of the Bcl-2 proapoptotic family recently shown to induce necrosis rather than apoptosis. (ox.ac.uk)

Northern blotting and in situ hybridization analysis has revealed that these factors are highly expressed in human tumors compared with normal tissue and that BNIP3 is up-regulated in perinecrotic regions of the tumor. (ox.ac.uk)
Isolation of specific targeted regions of the genome (all coding exons, immunoglobulin switching regions, regions identified by association studies) by long PCR or hybridization to oligonucleotide synthesized on arrays. (elimbio.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)
In order to gain a more comprehensive perspective on the physiology and regulation of the AlTR, we compared differential gene expression and protein content of cells adapted at pH 9.5 and un-adapted cells (pH 7.0) using complementary DNA (cDNA) microarray and two-dimensional (2D) gel electrophoresis, (combined with mass spectrometry) respectively. (essex.ac.uk)

With the public availability of data tools for their analysis were quickly developed and described in journals such as Nucleic Acids Research which published specialized issues on bioinformatics tools as early as 1982. (ind.in)

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)

The primary service of microbial arrays has been characterization of agents propagated to high titer in vitro ( 6 ). (cdc.gov)
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)

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)
Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes 10403S. (essex.ac.uk)
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)
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)

Here we report that a minimal combination of cis- regulatory sequences can support permanent RNA silencing of a single-copy transgene and its derivatives in C. elegans simply upon mating. (nature.com)
Recovery is also observed in most cases when double-stranded RNA is used to silence the same coding sequence in different regulatory contexts that drive germline expression. (nature.com)

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)

Annexin VII encodes a protein with a molecular weight of approximately 51 kDa with a unique, highly hydrophobic N-terminal domain of 167 amino acids and a conserved C-terminal region of 299 amino acids. (wikipedia.org)
Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)
These results clearly demonstrate that poly(A) tailing followed by cDNA sequencing is a powerful and less biased molecular ecological approach for the study of metabolically active microbial communities. (frontiersin.org)
Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. (genomicglossaries.com)
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)

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)
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)
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)

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)

Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
An antibody is used to precipitate a protein along with bound proteins. (genomicglossaries.com)

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. (nih.gov)
Sequencing of random-primed cDNA libraries from RNA fractions (nuclear, cytoplasmic, polyA, capped, or small RNA) provides a high-resolution map of all RNA species. (elimbio.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)

EDNs are synthesised as large precursor proteins that are post-translationally cleaved to the biologically active 21-amino acid form [ 3 ]. (biomedcentral.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)

Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. (ind.in)

Based on the miR microarray analysis, there were 14 miRs that showed significant differences (more than 2-fold) in expression between the 2 ESCC cells and non-malignant Het-1A. (biomedcentral.com)
Using cDNA arrays and serial analysis of gene expression, we found that hypoxia induces up-regulation of BNIP3 and its homologue, Nip3-like protein X. Analysis of human carcinoma cell lines showed that they are hypoxically regulated in many tumor types, as well as in endothelial cells and macrophages. (ox.ac.uk)
Regulation was hypoxia inducible factor-1-dependent, and hypoxia inducible factor-1 expression was suppressed by von Hippel-Lindau protein in normoxic cells. (ox.ac.uk)
When expressed as a fusion protein with eYFP in cultured cells, Sec31B-F associates with the endoplasmic reticulum and with vesicular-tubular clusters, displays restricted intracellular movement characteristic of COPII vesicle dynamics, co-distributes on organelles with Sec13, Sec31A and Sec23 (markers of the COPII coat), and concentrates with ts045-VSV-G-CFP (VSV-G) when examined early in the secretory pathway or after temperature or nocodazole inhibition. (biologists.com)
Analysis of PicoPLEX WGA products provided a correct diagnosis for 16/16 cells, with detection of 16/16 individual aneuploidies. (takarabio.com)

The DNA sample is divided into four separate sequencing reactions,containing all four of the standard deoxynucleotides(dATP, dGTP, dCTP, dTTP) and the DNA polymerase. (michaelperes.com)

the creation of a large number of compounds (usually proteins or peptides) through technologies such as phage display . (genomicglossaries.com)

The amplified DNA underwent exome capturing, followed by sequencing on both Illumina HiSeq® 2000 and Thermo Fisher Ion Proton platforms. (takarabio.com)
After gathering feedback from our customers and reviewing all Next Generation Sequencing platforms, we found that the Illumina platform is the current leader in Next Generation Sequencing. (elimbio.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)

Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. (nih.gov)
The poly(A) tailing method indicated that Desulfobacterales were the predominant Deltaproteobacteria, while most of the sequences in libraries constructed using RT-PCR were derived from Desulfuromonadales. (frontiersin.org)
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)
The prepared libraries are amplified into millions of clonal clusters, which are then sequenced one base at a time, in parallel, for each of the millions of clusters. (elimbio.com)

An alternatively spliced cassette exon results in two mRNA transcripts of 2.0 and 2.4 kb which are predicted to generate two protein isoforms differing in their N-terminal domain. (wikipedia.org)
PCR analysis of exon utilization reveals massive alternative mRNA splicing of Sec31B, with just 16 exons being constitutively utilized in all transcripts. (biologists.com)
The presence of a stop codon in exon 13 generates two families of Sec31B gene products (each displaying additional patterns of mRNA splicing): a group of full-length proteins (hereafter referred to as Sec31B-F) and also a group of truncated proteins (hereafter referred to as Sec31B-T), distinguished by their utilization of exon 13. (biologists.com)
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)

co-immunoprecipitation Used to determine protein- protein interactions . (genomicglossaries.com)
The pathway maps illustrate protein interactions and regulation to provide a comprehensive picture of signaling and disease processes. (bio-rad.com)
Protein-DNA or Protein-RNA Interactions (e.g. (elimbio.com)
Protein interactions of homeodomain proteins. (embl.de)
The recent structural determinations and biochemical analysis of several multimeric complexes have provided a better understanding of how protein interactions influence the DNA-binding activity of homeodomain proteins. (embl.de)

Sequencing of tags created by restriction digestion of cDNA generates gene expression profiles with an absolute count (from one to a few million) of the RNA in the sample. (elimbio.com)

p53 likely also plays a role given that p53 mutations are commonly found in advanced PC, and loss of wild-type protein function contributes to the phenotype of castration-resistant prostate cancer (CRPC). (oncotarget.com)

Thus, to address the challenge of more highly multiplexed differential diagnoses, we established an oligonucleotide microarray platform. (cdc.gov)
The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. (biomedcentral.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)

Dot blotting and dot hybridisation (4) evolved out of the filter hybridisation technique and provided the basic concept for DNA arrays. (ddw-online.com)

Author Manuscript and RNA repair protein AlkB-derived enzyme mixture was first used to remove methylations at the Watson-Crick face. (cdc.gov)

Tumor-infiltrated macrophages were isolated from human GC tissues using magnetic beads, gene transcription was determined by real-time PCR, protein expression was monitored using western blots, metabolites were determined using HPLC, and transcriptional regulation was analyzed by the luciferase-based reporter gene system. (cancerindex.org)
The basic format of the yeast-two hybrid system involves the creation of two hybrid molecules, one in which the " bait ' protein is fused with a transcription factor, and one in which the " prey " protein is fused with a related transcription factor . (genomicglossaries.com)

Despite the fact that the latest NGS technologies enable reading only of relatively short sequence fragments (~500 bp), these so-called "deep sequencing" methods are still powerful tools that ultimately may enable researchers to obtain a more holistic understanding of microbial communities in their natural environments ( Fuhrman, 2009 ). (frontiersin.org)
To visualize the fragments,the gel is exposed to X-ray film for autoradiography,yielding a series of dark bands each corresponding to a radiolabelled DNA fragment,from which the sequence may be inferred. (michaelperes.com)
The newly synthesized and labelled DNA fragments are heat denatured , and separated by size by gel electrophoresis on a denaturing polyacrylamide-urea gel with each of the four reactions run in one of the four individual lanes(lanes A, T, G,C), the DNA bands are then visualized by autoradiography or UV light,and the DNA sequence can be directly read off the X-ray film or gel image. (michaelperes.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)

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)
Rare mutations in genome sequence that result from failed DNA repair are transmitted across generations through DNA replication during each cell division. (nature.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)

Minimal primer dimer formation and genomic DNA cross reactivity. (bio-rad.com)
The technical variations of chain termination sequencing include tagging with nucleotides containing radioactive phosphorus for labelling, or using a primer labelled at the 5' end with a fluorescent dye. (michaelperes.com)
Dye- primer sequencing facilitates reading in an optical system for faster and more economical analysis and automation. (michaelperes.com)
Limitations include non-specific binding of the primer to the DNA,affecting accurate read-out of the DNA sequence,and DNA secondary structures affecting the fidelity of the sequence. (michaelperes.com)
Dye-terminator sequencing utilizes labelling of the chain terminator ddNTPs,which permits sequencing in a single reaction,rather than four reactions as in the labelled- primer method. (michaelperes.com)

A synthetic, specially- designed oligonucleotide with the ability to recognize and bind a protein ligand molecule or molecules with high affinity and specificity. (genomicglossaries.com)
Many homeodomain proteins require additional cofactors to bind with high affinity and specificity to their DNA sites. (embl.de)

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 algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. (biomedcentral.com)
Results IRE-like motifs were identified from genomic nucleic acid databases by an algorithm combining primary nucleic acid sequence and RNA structural criteria. (uni-wuerzburg.de)

One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed. (embl.de)

The observed variability between results of cDNA arrays and 2D gel electrophoresis may be accounted for by posttranslational modifications. (essex.ac.uk)

Amplicon sequence validated with next generation sequencing (NGS). (bio-rad.com)
3. What's the turn around time for Next Generation Sequencing samples? (elimbio.com)

Multiple signal transduction pathways are affected downstream from EDNRA/B. In the case of interaction of EDNs with EDNRA, a pertussis toxin-insensitive G protein becomes activated and promotes stimulation of phospholipase C, resulting in the transactivation of the mitogen-activated protein kinase pathway [ 13 ]. (biomedcentral.com)
This stable silencing requires components of the small RNA pathway and can silence homologous sequences in trans . (nature.com)

The base calling (sequencing data gathering) steps include incorporation of fluorophore-labeled nucleotides, fluorescence capture of the incorporated nucleotide, and cleavage of the fluorescence molecule. (elimbio.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)

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 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)
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)

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)
Here, we aimed at a first comprehensive analysis on EDN3 expression and its implication in human breast cancer. (biomedcentral.com)
A tissue microarray was used to study EDN3 protein expression in breast carcinoma (n = 150) and normal breast epithelium (n = 44). (biomedcentral.com)
Scope includes mutations and abnormal protein expression. (cancerindex.org)
Gene over-expression analyses in Xenopus limb and tail regeneration have indicated that successful regeneration requires the re-activation of developmental FGF or BMP signalling pathways [ 8 - 12 ]. (biomedcentral.com)
Furthermore, RNA-binding proteins can regulate the expression of Vv-circSIZ1. (bvsalud.org)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)

Anatomy7

Organisms7

Diseases3

Chemicals and Drugs48

Analytical, Diagnostic and Therapeutic Techniques and Equipment43

Phenomena and Processes93

Disciplines and Occupations3

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture2

Information Science9

Health Care7

Genes32

Microarrays15

Whole genome6

Advanced cDNA synthesis1

Genomes4

Human genome2

Synthesis8

RRNA gene sequences1

Primers4

Sanger3

Profiling1

Functional3

Microarray platforms1

Single Nucleotide3

Affymetrix GeneChip2

Apoptosis1

Hybridization2

Complementary2

Nucleic acids1

Reverse transcriptase1

Characterization2

Proteomic4

Regulatory2

Probes3

Molecular5

GDNA3

Approaches1

Antibody2

Species3

Amino acid2

Bioinformatics1

Cells5

Polymerase1

Peptides1

Illumina3

Libraries6

Exon4

Interactions5

Generates1

Phenotype1

Differential3

Hybridisation1

Enzyme1

Transcription2

Fragments3

Biological1

Genome sequence3

Primer5

High affinity and specificity2

Algorithm3

Motifs1

Posttranslational1

Next generation2

Pathway2

Nucleotides1

MRNA expression1

Cellular2

Quantitative2

Expression7