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  • genes
  • The information contained in the genome of an organism, its DNA, is expressed through transcription of its genes to RNA, in quantities determined by many internal and external factors. (helsinki.fi)
  • throughput
  • However, higher error rate, higher cost and lower throughput compared to the second-generation sequencing bring their own challenges. (helsinki.fi)
  • gene expression
  • Only on a single-cell level, can you eliminate the biological noise that is inherent to standard gene expression analysis - providing you the insights needed for a deeper understanding of transcription dynamics. (qiagen.com)
  • RNA sequencing (RNA-seq) has revolutionized the study of gene expression in animals, plants and microorganisms. (labroots.com)
  • To compare gene expression measures between 3'-RNA-seq and RNA-seq technologies, we used data from a subset of 20 samples that were previously used in a RNA-seq study of feed efficiency. (labroots.com)
  • In conclusion, 3'-RNA-seq is a cost effective method amenable to global gene expression studies at population-level, e.g., expression QTL (eQTL) mapping. (labroots.com)
  • We utilized weighted gene co-expression network analysis (WGCNA) to identify gene expression network modules associated with IA size and rupture. (ahajournals.org)
  • Affymetrix exon array and RNA-seq platforms, for generating large-scale exon-level gene expression profiling. (biomedcentral.com)
  • This problem can be circumvented by RNA-seq technology, which provides hypothesis-free single nucleotide resolution of gene expression so that, theoretically, any expressed sequence can be detected and quantified, given appropriate computational/statistical methods and sufficient sequencing depth. (biomedcentral.com)
  • Gene expression is highly tissue specific, therefore with traditional RNA capture methods one must be cautious in the interpretation of gene expression patterns, as they often reflect expression of a heterogeneous mix of cell populations. (wikipedia.org)
  • rRNA sequences
  • 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)
  • Many 16S rRNA sequences have been found which do not belong to any known cultured species, indicating that there are numerous non-isolated organisms. (wikipedia.org)
  • nucleotide
  • There are four main variation types: 5' trimming-the 5' dicing site is upstream or downstream from the reference miRNA sequence 3' trimming-the 3' dicing site is upstream or downstream from the reference miRNA sequence 3' nucleotide addition-nucleotides added to the 3' end of the reference miRNA nucleotide substitution-nucleotides changes from the miRNA precursor. (wikipedia.org)
  • The variations are mainly generated by a shift of Drosha and Dicer in the cleavage site, but also by nucleotide additions at the 3'-end, resulting new sequences different from the annotated miRNA. (wikipedia.org)
  • For known exRNA nucleotide sequences, RT-PCR can be applied to detect their presence within a sample as well as quantify their abundance. (wikipedia.org)
  • residues
  • Partial digestion of 3' or 5' labeled RNA with this enzyme thus generates a ladder of G residues. (thermofisher.com)
  • This suggests that tmRNA folding outside the TLD can be important, yet the pseudoknot region lacks conserved residues and pseudoknots are among the first structures to be lost as ssrA sequences diverge in plastid and endosymbiont lineages. (wikipedia.org)
  • phylogenetic
  • The method is evaluated with respect to accuracy, sensitivity to modified nucleotides in the template RNA, and phylogenetic usefulness, by examination of several 16S rRNAs whose gene sequences are known. (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)
  • Phylogenetic analysis based on 16S r-RNA sequence available from bacterial isolates was constructed. (nih.gov)
  • A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. (wikipedia.org)
  • The evolutionary origin of Telonema was inferred from phylogenetic reconstruction of single- and concatenated sequences obtained from both cultured strains and environmental clones (SSU only). (wikipedia.org)
  • pathways
  • Pathway analysis identified down-regulation of mitochondrial OXPHOS and upregulation of the inflammatory pathways in the Lmna-/- heart. (ahajournals.org)
  • Extracellular miRNAs are capable of targeting mRNAs in the recipient cell through RNA interference pathways. (wikipedia.org)
  • used Ingenuity Pathway Analysis (IPA) software that associated exRNAs found in human blood microvesicles with pathways involved in blood cell differentiation, metabolism, and immune function. (wikipedia.org)
  • bacterial
  • The 16S r-RNA sequence of isolated bacterial strain PSTB-1 has shown more homology with reported strain Enterobacter cloacae sub sp. (nih.gov)
  • Molecules
  • PCFGs have application in areas as diverse as natural language processing to the study the structure of RNA molecules and design of programming languages. (wikipedia.org)
  • downstream
  • Our analysis has characterized the technical features of the different library preparations, providing a necessary understanding of the costs and benefits of each method and the potential effects on the downstream analyses. (aacrjournals.org)
  • nucleotides
  • 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)
  • Nucleotides 4 to 26 of ebv-sisRNA-1 form a short hairpin loop that presents a Uridine-rich sequence motif (a possible platform for protein interactions) into the loop. (wikipedia.org)
  • characterization
  • Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, Lonnerberg P, Linnarsson S (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. (springer.com)
  • cells
  • Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, Lao K, Surani MA (2010) Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. (springer.com)
  • Given the absence of any detectable rearranged DNA in cells producing chimeric RNAs, the obvious explanation is the rearrangement at the RNA level. (biomedcentral.com)
  • Conventional sequencing begins with a culture of identical cells as a source of DNA. (wikipedia.org)
  • Indeed, ebv-sisRNA-1 is the third most abundantly produced EBV RNA after EBER1 and EBER2, which are highly expressed in EBV-infected cells. (wikipedia.org)
  • Both prokaryotic and eukaryotic cells are known to secrete RNA. (wikipedia.org)
  • to characterize exosomal RNA using the Agilent Bioanalyzer technology showed little to no trace of 18S and 28S rRNA in exosomes secreted by MC/9 murine mast cells, and similar conclusions were made by Skog et al. (wikipedia.org)
  • cellular
  • DAVID analyses showed that genes upregulated in an IA size-associated module were enriched with genes involved in cellular respiration and translation, while genes involved in transcription were down-regulated in a module associated with ruptured IAs. (ahajournals.org)
  • seawater
  • In 2002, Mya Breitbart, Forest Rohwer, and colleagues used environmental shotgun sequencing (see below) to show that 200 liters of seawater contains over 5000 different viruses. (wikipedia.org)
  • mechanism
  • In simulating the RNA cis-splicing mechanism, a cDNA is thought to be generated by trans-splicing when it is aligned to multiple non-contiguous genomic loci and the fusion junction obeys canonical GU-AG splice site. (biomedcentral.com)