Loading...
  • Expression
  • Expression quantitative trait loci in long non-coding RNA ZNRD1-AS1 influence both HBV infection and hepatocellular carcinoma development. (nih.gov)
  • Function
  • Although this polypeptide has the same function as the three nuclear DNA-directed RNA polymerases, it is more closely related to RNA polymerases of bacteriophage and mitochondrial polymerases of lower eukaryotes. (wikipedia.org)
  • rRNA
  • and that every sequence of bases in rRNA has information encoding more than one of these functions in addition to acting as a structural component of the ribosome. (theleagueofreason.co.uk)
  • A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16S rRNA or cloning of its gene. (pnas.org)
  • The 16S rRNA in bulk cellular RNA preparations is selectively targeted for dideoxynucleotide-terminated sequencing by using reverse transcriptase and synthetic oligodeoxynucleotide primers complementary to universally conserved 16S rRNA sequences. (pnas.org)
  • Three particularly useful priming sites, which provide access to the three major 16S rRNA structural domains, routinely yield 800-1000 nucleotides of 16S rRNA sequence. (pnas.org)
  • The relative simplicity of this approach should facilitate a rapid expansion of the 16S rRNA sequence collection available for phylogenetic analyses. (pnas.org)
  • 2017. Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence . (rutgers.edu)
  • The rRNA is removed because it represents over 90% of the RNA in a cell, which if kept would drown out other data in the transcriptome. (wikipedia.org)
  • functional
  • Maizel and coworkers [ 13 - 15 ] had hypothesized that biologically functional RNA structures may have more stable predicted secondary structures than would be expected for a random sequence of the same base composition. (biomedcentral.com)
  • The functional role of DI-like RNAs in natural infections remains to be established. (asm.org)
  • Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing. (ucdenver.edu)
  • RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks. (omictools.com)
  • Highly conserved DNA sequences are thought to have functional value, although the role for many highly conserved non-coding DNA sequences is poorly understood. (wikipedia.org)
  • Many functional sequences are also modular, containing regions which may be subject to independent selection pressures, such as protein domains. (wikipedia.org)
  • transcript
  • Although the small sample size prevents us from drawing definite conclusions, we observed promising novel co-expression networks for IAs: WCGNA analysis showed down-regulation of two transcript modules associated with ruptured IA status (r=-0.78, p=0.008 and r=-0.77, p=0.009), and up-regulation of two modules associated with aneurysm size (r=0.86, p=0.002 and r=0.9, p=4e-04), respectively. (ahajournals.org)
  • The stability and abundance of the shorter 3' transcript is confirmed in both Northern blotting and deep sequencing analysis. (wikipedia.org)
  • The editing site also overlaps with an antisense transcript which could also form a double stranded RNA structure creating a suitable substrate for ADARs. (wikipedia.org)
  • genomic
  • Badger & Olsen use the BLASTN program [ 17 ] to locate genomic regions with significant sequence similarity between two related bacterial species. (biomedcentral.com)
  • Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance," Journal of Pathology , vol. 237, no. 3, pp. 363-378, 2015. (hindawi.com)
  • degradation
  • The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. (wikipedia.org)
  • The amount of RNA degradation is checked with gel and capillary electrophoresis and is used to assign an RNA integrity number to the sample. (wikipedia.org)
  • tRNA
  • Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. (wikipedia.org)
  • The presence of pseudouridine in the mixed 10S RNA hinted that tmRNA has modified bases found also in tRNA. (wikipedia.org)
  • The similarity at the 3' end of tmRNA to the T stem-loop of tRNA was first recognized upon sequencing ssrA from Mycobacterium tuberculosis. (wikipedia.org)
  • Subsequent sequence comparison revealed the full tRNA-like domain (TLD) formed by the 5' and 3' ends of tmRNA, including the acceptor stem with elements like those in alanine tRNA that promote its aminoacylation by alanine-tRNA ligase. (wikipedia.org)
  • bacterial
  • In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing. (wikipedia.org)
  • Interactions
  • 2016. Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. . (rutgers.edu)
  • algorithm
  • Though we could confirm some anecdotal results where this was true, we were forced to the conclusion that in general, the predicted stability of structural RNAs is not sufficiently distinguishable from the predicted stability of random sequences to use as the basis for a reliable ncRNA genefinding algorithm. (biomedcentral.com)
  • The Inside-Outside algorithm is used in model parametrization to estimate prior frequencies observed from training sequences in the case of RNAs. (wikipedia.org)
  • Dynamic programming variants of the CYK algorithm find the Viterbi parse of a RNA sequence for a PCFG model. (wikipedia.org)
  • cellular
  • We present results for sequencing of cytoplasmic and nuclear RNA after cellular fractionation of tissue samples. (biomedcentral.com)
  • Our results show that cellular fractionation is a more rapid and cost effective approach than conventional polyA+ enrichment when studying mature RNAs. (biomedcentral.com)
  • RNA-Seq is used to analyze the continuously changing cellular transcriptome. (wikipedia.org)
  • The cellular RNA is selected based on the desired size range. (wikipedia.org)
  • genetic
  • I used to think that any knowledge of how that RNA world looked and what kinds of genetic machinery was contained within it, was forever obscured by the erasing nature of the accumulating mutations of time and the gradual replacement and loss of these primordially essential components. (theleagueofreason.co.uk)
  • The extent to which a sequence is conserved can be affected by varying selection pressures, its robustness to mutation, population size and genetic drift. (wikipedia.org)
  • citation needed] In coding sequences, the nucleic acid and amino acid sequence may be conserved to different extents, as the degeneracy of the genetic code means that synonymous mutations in a coding sequence do not affect the amino acid sequence of its protein product. (wikipedia.org)
  • amino acids
  • Within a sequence, amino acids that are important for folding, structural stability, or that form a binding site may be more highly conserved. (wikipedia.org)
  • The edited sites are found within the insulin growth factor binding domain of IGFBP7 and also Heparin binding domain.This region is also a site for proteolytic cleavage.Structural analysis of the edited sites determined that the two amino acids that corresponded to the edited sites are not directly involved in binding to IGF-1 but are found in regions flanking them. (wikipedia.org)
  • tissues
  • Thus, RNA-seq of separated cytosolic and nuclear RNA can significantly improve the analysis of complex transcriptomes from mammalian tissues. (biomedcentral.com)
  • A variety of parameters are considered when designing and conducting RNA-Seq experiments: Tissue specificity: Gene expression varies within and between tissues, and RNA-Seq measures this mix of cell types. (wikipedia.org)
  • transcriptome
  • Our new solutions for single-cell RNA-seq deliver a deeper understanding of the transcriptome, providing new biological insights. (qiagen.com)
  • Whole blood RNAseq analysis is a feasible tool to capture transcriptome dynamics and achieve a better understanding of the pathophysiology of IAs. (ahajournals.org)
  • Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome. (ucdenver.edu)
  • However, the precondition for large scale detection is a paired-end sequencing of the cell's transcriptome. (wikipedia.org)
  • RNA-Seq (RNA sequencing), also called whole transcriptome shotgun sequencing (WTSS), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment in time. (wikipedia.org)
  • viral
  • Using a sequencing approach, we characterize several subgenomic viral RNAs from human nasopharyngeal specimens infected with the influenza A(H1N1)pdm09 virus. (asm.org)
  • probabilistic
  • Probabilistic context free grammars (PCFGs) have been applied in probabilistic modeling of RNA structures almost 40 years after they were introduced in computational linguistics. (wikipedia.org)
  • tissue
  • A third candidate editing site did not show evidence of RNA editing in sequence analysis, which may be an indication that either the RNA editing process is tissue specific, or editing occurs at a low frequency. (wikipedia.org)
  • complementary
  • The editing complementary sequence (ECS) is located in a region within the coding sequence about 200 base pairs upstream from the editing sites.The ECS forms 140 bp duplex structure. (wikipedia.org)
  • stability
  • InvR has been shown to bind the RNA chaperone Hfq in vitro and Hfq is required for in vivo stability. (wikipedia.org)
  • typically
  • Gene discovery methods (whether experimental or computational) typically assume that the target is a protein coding gene that produces a messenger RNA. (biomedcentral.com)
  • Poly(A) selection is performed by mixing RNA with poly(T) oligomers covalently attached to a substrate, typically magnetic beads. (wikipedia.org)
  • intron
  • RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries. (wikipedia.org)
  • Viruses
  • Noroviruses (NoV) are a genetically diverse group of single-stranded positive-sense RNA, non-enveloped viruses belonging to the Caliciviridae family. (wikipedia.org)
  • metabolism
  • The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. (wikipedia.org)
  • methods
  • The family of SLAMseq Metabolic RNA labeling kits was successfully released in September this year accompanying the publication of the SLAMseq application in the Nature Methods journal. (delftenterprises.nl)
  • However, due to the slow mutation rates it experiences, it is often hard to distinguish between closely related species to any large degree, so other methods of analysis must be used. (wikipedia.org)
  • human
  • This is usually accomplished on human mitochondrial DNA by sequencing the hypervariable control regions (HVR1 or HVR2), and sometimes the complete molecule of the mitochondrial DNA, as a genealogical DNA test. (wikipedia.org)
  • data
  • data but I include it to remind myself for future analysis. (biostars.org)
  • The Netherlands - November 10, 2017 - Bluebee, a company driving genomic data-driven medicine, announces the successful integration of the SLAMdunk pipeline on Bluebee's private cloud-based platform, making it available to analyze data generated by every user of the SLAMseq Metabolic RNA Labeling Kit from Lexogen. (delftenterprises.nl)
  • Now all SLAMseq users will also have access to a secure, user-friendly and well-defined data analysis on Bluebee platform. (delftenterprises.nl)
  • Afterwards, we will load the full count matrix corresponding to all samples and all data, which is already provided in the same package, and will continue the analysis with that full table. (bioconductor.org)
  • The outstanding geophysical survey results provide the main data set for an important archaeological application of computerised network analysis. (wikipedia.org)
  • completely
  • Over-expression of PPARδ also sensitised THP-1 cells to phorbol ester and correspondingly, inhibition of PPARδ by anti-sense RNA completely abolished this response. (biomedcentral.com)
  • overall
  • Ultimately, using digital PCR to quantify NGS libraries decreases overall sequencing costs by ensuring an accurate quantification upfront, minimizing the need to re-run or repeat sequencing of samples. (thermofisher.com)
  • Species
  • Biologists can determine and then compare mtDNA sequences among different species and use the comparisons to build an evolutionary tree for the species examined. (wikipedia.org)
  • Role
  • Spinach is a synthetically derived RNA aptamer born out of the need for a way of studying the role of RNAs at the cellular level. (wikipedia.org)
  • complex
  • The need for fluorescently tracking RNA rose as its roles in complex cellular functions has grown to not only include mRNA, rRNA, and tRNA, but also RNAi, siRNA, snoRNA, and lncRNA, among others. (wikipedia.org)
  • high
  • Many derivatives of this structure were screened using SELEX, but the chosen fluorophore, 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), showed the best selective fluorescence with high quantum yield (0.72) when bound to the RNA sequence 24-2, deemed Spinach. (wikipedia.org)
  • Example
  • Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes the case. (wikipedia.org)
  • discover
  • The concept of the Mitochondrial Eve is based on the same type of analysis, attempting to discover the origin of humanity by tracking the lineage back in time. (wikipedia.org)
  • elements
  • The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation: a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn. (wikipedia.org)