• DEGs, or Differentially Expressed Genes, are genes whose expression levels show significant differences between two or more conditions or experimental groups. (pharmiweb.com)
  • It has become a prevalent technology, allowing an efficient genome-wide relative quantification of gene expression and, in particular, it is the method of choice to find differentially expressed genes between two or more biological conditions of interest. (frontiersin.org)
  • Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. (biomedcentral.com)
  • RNA-seq offers several advantages over microarrays or RT-qPCR for detecting differentially expressed genes (DEGs). (biomedcentral.com)
  • Differential gene expression analysis was performed with DESeq2, EdgeR, and Limma-Voom, and differentially expressed genes were annotated using BiomaRt. (pitt.edu)
  • Subgroup analysis showed that ER-β mRNA expression in ER+/PR+ breast tumors was significantly less than in ER+/PR− ( P = 0.009), ER−/PR+ ( P = 0.029), and ER−/PR− ( P = 0.023) groups. (aacrjournals.org)
  • Interestingly, the ER-β mRNA expression was specifically decreased by progestin in T-47D breast cancer cells. (aacrjournals.org)
  • Furthermore, the relative expression of ER-α and ER-β mRNA changes between normal human breast tissues and their concurrent matched ER+ breast tumors (6) , suggesting that altered expression of ER-α and ER-β occurs and may be functionally involved in breast tumorigenesis. (aacrjournals.org)
  • Interestingly, it also seemed that the level of ER-β mRNA varied among breast tumors but was not correlated with the expression of ER-α (4) , although the two receptor mRNAs were often coexpressed in the same tumor. (aacrjournals.org)
  • In this study, the relationship of ER-β mRNA expression to ER and PR status, as determined by ligand binding analysis, was investigated. (aacrjournals.org)
  • For example, the transcription, translation, and degradation of an mRNA is crucial to any gene expression event, and all three processes are controlled by a combination of elements including promoters, ribosome binding sites (RBSs), and cis -regulatory signals encoded in untranslated regions (UTRs). (universityofcalifornia.edu)
  • Chen J, Wang S, Jia S, Ding G, Jiang G, Cao L. Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profile in Pancreatic Cancer Derived Exosomes Treated Dendritic Cells by Microarray Analysis. (jcancer.org)
  • We used integrated lncRNA and mRNA microarrays to determine the expression profiles of PEX-treated DCs and normal DCs derived from five healthy donors. (jcancer.org)
  • For example, exosomes and nanovesicles secreted by living cells serve as intercellular couriers of mRNA, microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and proteins and have thus garnered considerable interest [ 3 ]. (jcancer.org)
  • Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy. (biomedcentral.com)
  • Whole-transcriptome sequencing (RNA-seq) technology has emerged as a revolutionary platform for genome-wide quantification of mRNA transcripts. (biomedcentral.com)
  • The C-terminal domain of YTHDF2 selectively binds to m6A-containing mRNA whereas the N-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. (scienceopen.com)
  • RNA sequencing (RNA-Seq) in CRC tissues and adjacent normal tissues from 6 CRC patients was performed and functional lncRNA-mRNA co-expression network was constructed afterwards. (biomedcentral.com)
  • In addition, 1448 lncRNA-mRNA co-expression pairs were screened out from 940,905 candidate lncRNA-mRNA pairs. (biomedcentral.com)
  • lncRNA-AK058003 can reduce mRNA stabilizing protein HuR, which results in the inhibition of the expression of γ-synuclein. (oncotarget.com)
  • Collectively, lncRNA-AK058003 can reduce the expression of mRNA stabilizing protein HuR and act as a precursor of miR-15a to suppress γ-synuclein-mediated cell proliferation and the metastasis of hepatocellular carcinoma. (oncotarget.com)
  • RNA-based strategies offer a series of novel therapeutic applications, including altered processing of the target pre-mRNA transcript, reprogramming of genetic defects through mRNA repair, and the targeted silencing of allele- or isoform-specific gene transcripts. (ox.ac.uk)
  • This review examines the potential of RNA therapeutics, focusing on antisense oligonucleotide modification of pre-mRNA splicing, methods for pre-mRNA trans-splicing, and the isoform- and allele-specific applications of RNA interference. (ox.ac.uk)
  • Our RNA service includes mRNA and total RNA library preparation and sequencing on Illumina platforms. (lu.se)
  • a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. (frontiersin.org)
  • Our goal is to understand the molecular mechanisms whereby the genomic RNA of influenza-like viruses is, on the one hand, the template for transcription and replication of the viral genome by its RNA-dependent RNA polymerase and, on the other hand, an Achilles' heel, whose recognition as non-self can trigger an innate immune response to counter the viral infection. (embl.org)
  • Studies of genes transcribed by RNA polymerase II (Pol II) have shown that open and closed chromatin structures are dynamically regulated through multiple mechanisms, including histone modifications, histone variant incorporation, and DNA methylation (reviewed in reference 17 ). (asm.org)
  • Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to validate the expression pattern of differentially expressed lncRNAs. (biomedcentral.com)
  • Eukaryotic 5S rRNA is synthesized by RNA polymerase III, whereas other eukaryotic rRNAs are cleaved from a 45S precursor transcribed by RNA polymerase I. In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. (wikipedia.org)
  • The AAV non-coding RNA expression vector uses an RNA polymerase II promoter to drive the expression of the user-selected non-coding RNA gene. (vectorbuilder.kr)
  • For RNA polymerase II-mediated transcription, the start site is typically in the 3' region of the promoter while the termination site is within the polyA signal sequence. (vectorbuilder.kr)
  • This gene was tagged by insertion of the Tc1 transposon, and the wild-type gene was cloned by chromosomal walking 11 kb from ama-1, a cloned gene encoding the large subunit of RNA polymerase II. (ncsu.edu)
  • The orf2 codes for the capsid logic data such as sex, age, clinical classification (loca- protein and the orf3 codes for an RNA-dependent tion, severity, and number of lesions), and province of RNA polymerase (RdRp). (cdc.gov)
  • In genetics and genomics research, gene expression refers to the process by which information encoded in a gene's DNA sequence is converted into functional proteins or RNA molecules. (pharmiweb.com)
  • Mechanically, m6A can be recognized by "reader" proteins or can directly modify RNA conformation, and it widely affects gene expression by mediating RNA stability, translation, splicing and export. (scienceopen.com)
  • The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
  • Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
  • More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
  • Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)
  • Although all the currently known ASD risk genes code for proteins, long non-coding RNAs (lncRNAs) as essential regulators of gene expression have been implicated in ASD. (figshare.com)
  • In bacteria and archaea, the large ribosomal subunit (LSU) itself is composed of two RNA moieties, the 5S rRNA and another larger RNA known as 23S rRNA, along with numerous associated proteins. (wikipedia.org)
  • In silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA-binding proteins in Aedes aegypti. (bvsalud.org)
  • RNA-binding proteins (RBPs) are the proteins that bind RNAs and regulate their functioning. (bvsalud.org)
  • In this study, we screened the whole genome of Aedes aegypti , the primary vector of several pathogenic viruses , and identified the proteins containing RNA recognition motif (RRM), the most abundant protein domain in eukaryotes . (bvsalud.org)
  • While the specific function of polyglutamine-binding protein 1 is not well understood, it is believed to play a role in processing and transporting RNA, a chemical cousin of DNA that serves as the genetic blueprint for the production of proteins. (medlineplus.gov)
  • The RNA is held within the granules until the genetic information it carries is translated to produce proteins or until cellular signals or environmental factors trigger the RNA to be degraded. (medlineplus.gov)
  • The program collects whole-genome sequence and other -omics data (In biology, -omics refers to measurable differences or changes in biological molecules, such as genes, metabolites, proteins, and RNA. (cdc.gov)
  • The expression profiles of long noncoding RNAs (lncRNAs) and mRNAs of PEX-treated dendritic cells are unknown. (jcancer.org)
  • To our knowledge, this is the first study to detect the differential expression of lncRNAs and mRNAs associated with PEX-treated DCs. (jcancer.org)
  • The current study aimed to evaluate the expression pattern of lncRNAs and messenger RNAs (mRNAs). (biomedcentral.com)
  • Finally, RT-qPCR results verified the expression pattern of lncRNAs, as well as the relationships between lncRNAs and mRNAs in 60 pairs of CRC tissues. (biomedcentral.com)
  • sRNAs usually work by pairing with target mRNAs, often with the assistance of protein partners called RNA chaperones. (nature.com)
  • RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. (biorxiv.org)
  • Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. (biomedcentral.com)
  • To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). (biomedcentral.com)
  • This technique enables the sequencing of all RNA molecules in a high-throughput manner. (biomedcentral.com)
  • Due to the development of RNA sequencing technology, the distribution pattern of m6A in the transcriptome has been uncovered. (scienceopen.com)
  • Library preparation can be a source of bias in RNA-sequencing studies, leading to false positives in genes identified as differentially expressed between conditions. (pitt.edu)
  • This study aims to illustrate the impact of using different library preparations in RNA sequencing. (pitt.edu)
  • The Kim lab recently completed RNA sequencing analysis to measure the dysregulation of genes in response to these factors in zebrafish embryos. (umaine.edu)
  • Twelve samples (harboring 6 CRC tissues and 6 paired adjacent normal tissues) used in RNA-Sequencing (RNA-Seq) were collected from six Chinese patients who were diagnosed with stage II b or IIIb CRC. (biomedcentral.com)
  • Ribosomal RNA was removed and the sequencing library was generated using Hieff NGS® MaxUp rRNA Depletion Kit (Yeasen, China) following manufacturer's recommendations. (biomedcentral.com)
  • Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. (nature.com)
  • Weighing each method's performance and ease, we identified the dUTP second-strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing. (nature.com)
  • Annotating genomes with massive-scale RNA sequencing. (nature.com)
  • RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. (biomedcentral.com)
  • Given increasing numbers of RNA-seq samples in the public domain, we here studied to what extent eQTLs and ASE effects can be identified when using public RNA-seq data while deriving the genotypes from the RNA-sequencing reads themselves. (biomedcentral.com)
  • Given the exponential growth of the number of publicly available RNA-seq samples, we expect this approach will become especially relevant for studying the effects of tissue-specific and rare pathogenic genetic variants to aid clinical interpretation of exome and genome sequencing. (biomedcentral.com)
  • Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects. (crossref.org)
  • Immuno-oncology gene expression profiling of FFPE clear cell renal cell carcinoma: Performance comparison of the NanoString nCounter technology with targeted RNA sequencing. (expressionpathology.com)
  • Obtain ultra-sensitive digital expression profiling data for all 19,000 protein-coding genes in the human genome or some 5000 mouse genes with our DriverMap Targeted RNA Sequencing platform. (cellecta.com)
  • QIAseq Targeted RNA Indices are for indexing samples for targeted RNA sequencing and primers necessary for sequencing RNA libraries generated by QIAseq Targeted RNA Panels. (qiagen.com)
  • Innovative UMIs (unique molecular indices) eliminate PCR duplication and amplification bias to deliver the most accurate results (see figure Unbiased and accurate gene quantification (A) Different amounts (20 ng, 5 ng or 1.25 ng) of universal reference RNA were used to determine expression levels of three genes (BNIP1, CTNND2 and DAPK1) using targeted RNAseq. QIAseq digital RNA sequencing method (A; molecular barcode counts) showed accurate quantification of all three genes corresponding to different RNA input, whereas traditional targeted RNAseq (B; read counts) revealed PCR duplication limitation and yielded inaccurate quantification. "> Unbiased and accurate gene quantification ). (qiagen.com)
  • The unique combination of our proprietary primer design algorithm and rigorous testing of every primer assay guarantees high specificity and accurate results (see figure Proprietary primer design delivers gene-specific amplicons (>97% specificity) Sequencing libraries were prepared using 1.25, 5 or 20 ng universal reference RNA and QIAseq Targeted RNA Panels, ranging from 12-plex to 1000-plex. Sequencing was performed on the Illumina MiSeq, dedicating 1 million reads per sample. Specificity is calculated as percent of trimmed and mapped reads that map to intended targets. "> Proprietary primer design delivers gene-specific amplicons - 97% specificity ). (qiagen.com)
  • The QIAseq Targeted RNA Panel workflow has been optimized to deliver highly uniform sequencing results, to ensure sequencing capacity is utilized very efficiently. (qiagen.com)
  • Targeted RNA sequencing using UMIs is optimized to deliver highly reliable quantification down to ~100 copies of an RNA target in 25 ng total RNA (see figure Positive results with as little as 0.2 copies of RNA per cell ERCC standards, at 86 to 705,500 copies, spiked into universal reference RNA sample and enriched using 384-plex QIASeq Targeted RNA Panel in three technical replicates. (A) Sensitivity measurement. Under standard conditions (20 ng RNA input, 0.5 million MiSeq reads), ≥~100 copies of ERCC transcripts were reliability detected, which is the equivalent of ~0.2 copies per cell. (B) Precision measurement. At >10 barcodes/gene, CV was less than 5% for all targets, indicating high technical reproducibility. This corresponds to ~100 copies target RNA in the sample. "> Positive results with as little as 0.2 copies of RNA per cell ). (qiagen.com)
  • Expression analysis of the genes encoding RBPs using publicly available RNA sequencing data for different developmental time points of the mosquito life cycle starting from the ovary and eggs up to the adults revealed stage-specific expression with several genes preferentially expressed in early embryonic stages and blood -fed female ovaries . (bvsalud.org)
  • Using bulk RNA-sequencing from whole blood, we examined the association between gene expression and WTC-related PTSD symptom severity on (i) highest lifetime Clinician-Administered PTSD Scale (CAPS) score, (ii) past-month CAPS score, and (iii) PTSD symptom dimensions using a 5-factor model of re-experiencing, avoidance, emotional numbing, dysphoric arousal and anxious arousal symptoms. (cdc.gov)
  • Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study. (cdc.gov)
  • Increasingly, whole genome sequencing is being used with other analytic measures (DNA methylation, RNA expression, metabolite profiles) in large-scale collaborative initiatives. (cdc.gov)
  • High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (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)
  • 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)
  • Another plasmid-encoded ProQ/FinO family member, FopA, has also been shown to interact with a single antisense RNA 11 . (nature.com)
  • Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have recently emerged as important regulators of protein translation and shown to have diverse biological functions. (ncbs.res.in)
  • We demonstrate that specific 5'-tsRNAs can preferentially interact with the RNA-binding protein, Igf2bp1, in the RA-induced differentiated state. (ncbs.res.in)
  • One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. (mdpi.com)
  • The Cusack group uses X-ray crystallography and cryo electron-microscopy (cryoEM) to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. (embl.org)
  • For development of greater modularity, we extend the use of synthetic self-cleaving ribozyme switches to detect changes in input protein levels and convey that information into programmed gene expression in eukaryotic cells. (caltech.edu)
  • We demonstrate both up- and down-regulation of levels of an output transgene by more than 4-fold in response to rising input protein levels, with maximal output gene expression approaching the highest levels observed in yeast. (caltech.edu)
  • Our switch devices do not depend on special input protein activity, and can be tailored to respond to any input protein to which a suitable RNA aptamer can be developed. (caltech.edu)
  • Genetic systems often behave unpredictably due to structural interactions between DNA, RNA and protein components as well as functional interactions with host factors and metabolites. (universityofcalifornia.edu)
  • However, measuring gene expression profiles in whole blood samples can be complicated because of the high protein and enzyme abundancy that affect the stability and quality of the RNA. (eur.nl)
  • Although expression of non-protein-coding RNA (ncRNA) can be altered in human cancers, their functional relevance is unknown. (gla.ac.uk)
  • Although uc.338 is partially located within the poly(rC) binding protein 2 (PCBP2) gene, the transcribed ncRNA encoding uc.338 is expressed independently of PCBP2 and was cloned as a 590-bp RNA gene, termed TUC338. (gla.ac.uk)
  • Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
  • Interaction of 5S rRNA with the La protein prevents the RNA from degradation by exonucleases in the cell. (wikipedia.org)
  • La protein is found in the nucleus in all eukaryotic organisms and associates with several types of RNAs transcribed by RNA pol III. (wikipedia.org)
  • La protein interacts with these RNAs (including the 5S rRNA) through their 3' oligo-uridine tract, aiding stability and folding of the RNA. (wikipedia.org)
  • The DriverMap Targeted RNA Expression Profiling Service measures the expression level of all 19,000 protein-coding genes in the human genome or almost 5000 mouse genes from just a few picograms of total RNA. (cellecta.com)
  • such as those in the brain, polyglutamine-binding protein 1 is found in structures called RNA granules. (medlineplus.gov)
  • Through these mechanisms, polyglutamine-binding protein 1 is thought to help control the way genetic information is used (gene expression) in neurons. (medlineplus.gov)
  • The function of a shortened or otherwise abnormal protein is likely impaired and interferes with normal gene expression in neurons, resulting in abnormal development of the brain and the signs and symptoms of Renpenning syndrome. (medlineplus.gov)
  • Overview of Genetics A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
  • Author Manuscript and RNA repair protein AlkB-derived enzyme mixture was first used to remove methylations at the Watson-Crick face. (cdc.gov)
  • RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. (frontiersin.org)
  • The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq. (biomedcentral.com)
  • Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. (biomedcentral.com)
  • As one of the most widely used tools for transcriptome profiling, quantification of differential gene expression has played a pivotal role in the identification of pathway and gene-network interactions [ 1 - 3 ]. (biomedcentral.com)
  • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. (nature.com)
  • Using these reads we performed gene expression quantification. (biomedcentral.com)
  • Assembly of the alignments into full transcripts and quantification of the expression levels of each gene/transcript. (lu.se)
  • assigns single-cell RNA-seq expression to cancer clones by probabilistically mapping RNA-seq to clone-specific copy number profiles using reparametrization gradient variational inference . (github.com)
  • In contrast, Single-cell RNA-seq measures the expression cell by cell which adds more detail to the analysis. (biobam.com)
  • Applied to differential expression analysis, Single-cell RNA-seq not only allows to test between samples and conditions but also between cell types, thus adding more complexity to the analysis. (biobam.com)
  • Previous to the differential expression analysis, a Single-cell RNA-Seq Clustering was performed using OmicsBox, which resulted in 9 different clusters ( Figure 1) . (biobam.com)
  • This post is meant to help design the most appropriate configuration for your Single-cell RNA-seq Differential Expression Analysis using OmicsBox. (biobam.com)
  • Non-coding RNAs (ncRNAs), mainly including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), can function as important regulators in gene expression. (biomedcentral.com)
  • In nature, the control of the activity of an RNA transcript is crucial to its function. (universityofcalifornia.edu)
  • However, regulatory elements can unpredictably interact with each other through the formation of RNA structures and the recruitment of factors that affect global transcript accessibility and stability. (universityofcalifornia.edu)
  • Both developmental brain gene expression data and transcript sequence were found to contain relevant information for ASD risk gene prediction. (figshare.com)
  • During the pre-training phase of model construction, an autoencoder network was implemented for a representation learning of the gene expression data, and a random-forest-based feature selection was applied to the transcript-sequence-derived k-mers. (figshare.com)
  • Conclusions Our results suggest that ASD risk genes can be accurately predicted using developmental brain gene expression data and transcript sequence features, and the models may provide useful information for functional characterization of the candidate lncRNAs associated with ASD. (figshare.com)
  • Binding between 5S rRNA and TFIIIA serves to both repress further transcription of the 5S RNA gene and stabilize the 5S RNA transcript until it is required for ribosome assembly. (wikipedia.org)
  • As a result, the transcript generated from this vector does not correspond precisely to the selected non-coding RNA gene, but contains some additional sequences both upstream and downstream. (vectorbuilder.kr)
  • Alternative approaches targeting RNA have the potential to circumvent some of these difficulties, particularly as the active therapeutic molecules are usually short oligonucleotides and the target gene transcript is under endogenous regulation. (ox.ac.uk)
  • Statistical methods are employed to identify genes that exhibit significant changes in expression between experimental conditions. (pharmiweb.com)
  • After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. (frontiersin.org)
  • Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. (biomedcentral.com)
  • Methods and/or tools to facilitate the combination of various regulatory elements originating from various different sources to predictably control the activity of any desired RNA would be beneficial for numerous biotechnology applications. (universityofcalifornia.edu)
  • All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. (biomedcentral.com)
  • Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. (biomedcentral.com)
  • Although biochemical studies indicate that N(6)-methyladenosine (m(6)A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. (scienceopen.com)
  • There are multiple published methods for strand-specific RNA-seq, but no consensus exists as to how to choose between them. (nature.com)
  • Figure 1: Methods for strand-specific RNA-seq. (nature.com)
  • 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)
  • Methods for analysis of gene expression: microarray, hybridisation, promoter analyses. (lu.se)
  • We demonstrate here that statistical adjustment employing existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. (biorxiv.org)
  • Using RNA-seq data from a molecular degradation experiment of human brain tissue, we introduce the quality surrogate variable (qSVA) analysis framework for estimating and removing the confounding effect of RNA quality in differential expression analysis. (biorxiv.org)
  • With regard to C5aR1, it has been shown that C5aR1 antagonism in a murine AD model improves histological and cognitive outcomes, and is associated with decreased inflammatory signaling and enhanced expression of degradation/clearance pathways (41). (nos-nop.org)
  • Freeze and thaw samples as few times as possible and work with the RNA on ice to avoid degradation. (lu.se)
  • Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. (mdpi.com)
  • These studies are being extended to viral RNPs (the physiological RNA synthesis units) to understand the behaviour of the viral nucleoprotein during replication and transcription and to include host factors important for viral replication. (embl.org)
  • Synthesis of AR1 RNA was dependent on T-DNA transfer and TGMV DNA replication, demonstrating that it is a plant transcription product. (ncsu.edu)
  • The ratio between AR1 RNA and the major leftward RNA was constant and was used to normalize AR1 transcription for viral DNA copy number. (ncsu.edu)
  • Our data reveal the differential expression landscape of 493 transcription factors and 682 lncRNAs and highlight specific expression clusters operating in HSCs. (lu.se)
  • Molecular mechanisms for regulation of gene expression at different levels: remodeling of chromatin, initiation of transcription, nuclear transport and signalling, and RNA interference. (lu.se)
  • With RNA-seq , we can capture and quantify the abundance of transcripts, revealing the dynamic landscape of gene expression within a cell or tissue. (pharmiweb.com)
  • We used agroinoculation of petunia leaf discs with the A component to develop a transient expression system which permits direct examination of viral transcripts by S1 nuclease protection. (ncsu.edu)
  • When studying gene expression, researchers often compare gene expression profiles between different biological samples or experimental conditions, such as healthy and diseased tissues, treated and untreated cells, or different developmental stages. (pharmiweb.com)
  • Expression was verified in cell lines by real-time PCR or in tissues by in situ hybridization using tissue microarrays. (gla.ac.uk)
  • Total RNA was extracted from tissues with TRIzol as per the manufacturer's protocol (Invitrogen, USA). (biomedcentral.com)
  • 4,978 public human RNA-seq runs, representing many different tissues and cell-types, passed quality control. (biomedcentral.com)
  • A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq. (crossref.org)
  • As a result of this characteristic, it is possible to identify groups of cells with different expression patterns inside the tissues, which putatively correspond to different cell types. (biobam.com)
  • The 5S ribosomal RNA (5S rRNA) is an approximately 120 nucleotide-long ribosomal RNA molecule with a mass of 40 kDa. (wikipedia.org)
  • Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat. (ncsu.edu)
  • Chromatin structure and expression of plant ribosomal RNA genes. (ncsu.edu)
  • This is very different from RNA-Seq, where you essentially sequence the entire transcriptome. (cellecta.com)
  • Dynamic expression of tRNA-derived small RNAs define cellular states. (ncbs.res.in)
  • Cellular ucRNA expression was modulated with siRNAs, and the effects on global gene expression and growth of human and murine HCC cells were evaluated. (gla.ac.uk)
  • By subjecting DEGs to gene ontology enrichment analysis, pathway analysis, or functional annotation, we gain insights into the biological processes, molecular functions, and pathways associated with the observed gene expression changes. (pharmiweb.com)
  • Conservation of gene sequences across species may indicate an essential functional role, and therefore we evaluated the expression of ultraconserved RNAs (ucRNA) in hepatocellular cancer (HCC). (gla.ac.uk)
  • We have extended our work on viral polymerases to those of other segmented negative-strand RNA viruses such as the large order of Bunyavirales . (embl.org)
  • Accumulating evidence shows that tRNA expression and mutations are associated with various diseases such as neurological pathologies and cancer development3,4. (cdc.gov)
  • This platform can potentially be employed to regulate the expression of any transgene or any endogenous gene by 3' UTR replacement, allowing for more complex cell state-specific reprogramming. (caltech.edu)
  • Many ncRNAs have critical roles in tumorigenesis, and some ncRNAs function as competing endogenous RNAs (ceRNAs) to perturb gene expression. (biomedcentral.com)
  • The organisms studied in dual-species transcriptomics experiments are present in different relative abundances and while the read proportions between the two organisms differ by system, most infection models, particularly biologically relevant models, have the total RNA content of the host vastly outnumbering microbe [ 15 ]. (biomedcentral.com)
  • TaKaRa SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian for low input and poor quality samples. (lu.se)
  • To understand how the immune system is being modulated by these factors the role of non-coding RNAs (ncRNA) were investigated. (umaine.edu)
  • DMRs show continuous gain or loss of methylation during differentiation, and the overall change in DNA methylation correlates inversely with gene expression at key loci. (lu.se)
  • N6-methyladenosine (m6A) is the most abundant inner RNA modification in eukaryotes. (scienceopen.com)
  • The Kim lab is particularly interested in the role of micro-RNAs (miRNA) and long intergenic non-coding RNAs (lincRNAs). (umaine.edu)
  • How to Do Differential Gene Expression Analysis? (pharmiweb.com)
  • Differential Gene Expression analysis is a fundamental tool for identifying genes whose expression levels significantly differ between experimental conditions or biological samples. (pharmiweb.com)
  • Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from the human brain. (biorxiv.org)
  • In this study, we determined for the first time the expression of lncRNA ANRIL in human HCC by quantitative Real-time-PCR analysis. (nih.gov)
  • Expression analysis of tsRNAs in distinct heterologous cell and tissue models of stem vs. differentiated states revealed a differentiation-dependent enrichment of 5'-tsRNAs. (ncbs.res.in)
  • With this increasing complexity, best practices are needed for properly designing and conducting a differential expression analysis within a multi-species transcriptomics experiment. (biomedcentral.com)
  • Here, we describe best practices for multi-species transcriptomics experiments from the initial experimental design to the downstream differential expression analysis, highlighting important considerations that should be taken for these multi-species analyses when compared to traditional single-species transcriptomics analyses. (biomedcentral.com)
  • Gene expression profiles of PBMCs were compared to that of Tempus tubes using the Advanced Analysis module of nSolver software. (eur.nl)
  • MicroScope is a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network visualization. (biostars.org)
  • These results indicate that library preparation influences differential gene expression analysis and subsequently affects the downstream analyses that investigate the biological pathways impacted by gene expression level. (pitt.edu)
  • In conclusion, these results of the RNA-seq and bioinformatic analysis strongly suggested that the dysregulation of lncRNA is involved in the complicated process of CRC development, and providing important insight regarding the lncRNAs involved in CRC. (biomedcentral.com)
  • Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)
  • Scholars@Duke publication: Immunofluorescent analysis of expression of the RNA tumor virus major glycoprotein, gp71, on the surfaces of normal murine cells. (duke.edu)
  • The differential expression (DE) analysis has been used in bulk RNA-seq analysis for many years. (biobam.com)
  • With bulk RNA-seq analysis many cells are sequenced at the same time, so gene expression levels are commonly measured at the tissue level. (biobam.com)
  • The analysis includes deconvolution and normalization of the expression levels for each target gene. (cellecta.com)
  • The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants. (ncsu.edu)
  • Analysis of gene expression from these individuals can help in identifying biomarkers of PTSD. (cdc.gov)
  • GBCdb will help to elucidate the potential biological roles of different RNAs and allow for the exploration of RNA interactions in GBC. (biomedcentral.com)
  • Sci Rep. 2018) and nucleoside analogue, RNA synthesis inhibitors (Kouba et al . (embl.org)
  • Long non-coding RNAs (lncRNAs ) are widely involved in the pathogenesis of cancers. (biomedcentral.com)
  • Here we developed a comprehensive computational pipeline to compare library quality metrics from any RNA-seq method. (nature.com)
  • Raw RNA-seq data contains a wealth of information but requires preprocessing steps to ensure accurate and reliable results. (pharmiweb.com)
  • Cancer RNA Expression Market research Report is an inestimable supply of insightful data for business strategists. (express-press-release.net)
  • Finally, we recommend to RNA-Seq practitioners the production of a pilot data set to strictly analyze the power of their experimental design, or the use of a public data set, which should be similar to the data set they will obtain. (frontiersin.org)
  • The data suggest the possibility that expression of ER-β in human breast tumors is a marker of endocrine therapy responsiveness. (aacrjournals.org)
  • A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
  • Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson's r = 0.92) and Ion Torrent Proton (Pearson's r = 0.92). (biomedcentral.com)
  • Herein, to provide better understanding of the molecular events in GBC pathogenesis, we developed GBCdb ( http://tmliang.cn/gbc/ ), a user-friendly interface for the query and browsing of GBC-associated genes and RNA interaction networks using published multi-omics data, which also included experimentally supported data from different molecular levels. (biomedcentral.com)
  • By deriving and imputing genotypes from RNA-seq data, it is possible to identify both eQTLs and ASE effects. (biomedcentral.com)
  • Fortunately, the raw data of many RNA-seq experiments are being deposited in public databases, and the number of available human RNA-seq samples is growing exponentially, for example, in the European Nucleotide Archive (ENA) (Figure 1 a). (biomedcentral.com)
  • Thanks to applying DE to Single-cell data, it is possible to look for differences in gene expression between. (biobam.com)
  • In addition, in order to phenotypically anchor the gene expression data, changes in the heterogeneity of cell subtype populations and cell cycle phase were monitored using flow cytometry. (plos.org)
  • Our data have provided evidence for a comparable prediction of clinical outcome in CMF-treated breast cancer patients using conventional clinical variables and gene expression based markers. (lu.se)
  • Subsequently, immune-related gene expression was profiled using the PanCancer Immune Profiling Panel of NanoString technology. (eur.nl)
  • We found marked differences in strand specificity, library complexity, evenness and continuity of coverage, agreement with known annotations and accuracy for expression profiling. (nature.com)
  • Figure 6: Digital expression profiling using strand-specific RNA-seq. (nature.com)
  • Cellecta's DriverMap™ service is a novel, comprehensive end-to-end, whole-genome targeted expression profiling solution intended for research applications. (cellecta.com)
  • QIAseq Targeted RNA Panels have been developed as a Sample to Insight solution for quantitative gene expression profiling using RNAseq. (qiagen.com)
  • The cell counters RNA viruses with innate immune pattern-recognition receptors, such as the RNA helicase RIG-I, which recognise particular viral RNA structural motifs (e.g. 5′ triphosphate-dsRNA) as non-self, thus activating a signalling pathway leading to interferon production and establishment of the anti-viral state. (embl.org)
  • An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. (scienceopen.com)
  • Though accepted as the gold-standard for measuring gene expression, this method is lower throughput and not amenable to perform global expression analyses. (biomedcentral.com)
  • A number of RNA-Seq quality control analyses summarized in FastQC and MultiQC reports. (lu.se)
  • Once the reads are mapped, we quantify the expression level of each gene. (pharmiweb.com)
  • However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. (biomedcentral.com)
  • We downloaded the raw reads for all available human RNA-seq datasets. (biomedcentral.com)
  • We also derived genotypes using the RNA-seq reads and used imputation to infer non-coding variants. (biomedcentral.com)
  • As a result, with the DriverMap assay, you can achieve a very good depth of coverage and more sensitivity than RNA-Seq, with 5-10 fold fewer reads. (cellecta.com)
  • Epigenetic and RNA-mediated mechanisms. (lu.se)
  • Our findings provide a platform to improve understanding of the detailed multi-omics RNA landscapes of GBC, especially for GBC-associated RNA interactions, which will support future studies on cancer treatment. (biomedcentral.com)
  • Transient expression of heterologous RNAs using tomato golden mosaic virus. (ncsu.edu)
  • The bacterial genes encoding chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) were transiently expressed in leaf discs from the AR1 promoter in TGMV A. The levels of AR1 and GUS RNAs were similar in leaf discs after adjusting for viral DNA copy number, while CAT RNA was less abundant. (ncsu.edu)
  • Finally, we explored public datasets to demonstrate potential RNA quality confounding when comparing expression levels of different brain regions and diagnostic groups beyond schizophrenia. (biorxiv.org)
  • long non-coding RNA ANRIL (lncRNA ANRIL) has been demonstrated to play a crucial role in cancer progression. (nih.gov)
  • Long non-coding RNAs (lncRNAs) have been identified as critical players in multiple cancers and lncRNAs are tightly linked to cancer progression. (oncotarget.com)
  • GenePaint.org: an atlas of gene expression patterns in the mouse embryo. (jax.org)
  • By comparing gene expression patterns during embryogenesis or tissue differentiation, we unravel the molecular events that shape organisms, advancing our understanding of developmental biology. (pharmiweb.com)
  • When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. (biomedcentral.com)
  • Silencing the m(6)A methyltransferase significantly affects gene expression and alternative splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. (scienceopen.com)
  • This walkthrough illustrates how GBrowse and the RNA-Seq tools at FlyBase can be used to identify genes with similar expression patterns. (thegep.org)
  • Each cluster consists of a group of cells with similar expression patterns. (biobam.com)
  • That means that, although identified as different clusters, they have similar expression patterns. (biobam.com)
  • Blood samples were collected in both EDTA tubes, and Tempus tubes containing an RNA stabilizer (total n = 48). (eur.nl)
  • Both types of samples provided good quality RNA and gene expression measurements. (eur.nl)
  • We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). (biomedcentral.com)
  • parasite isolates from eishmania RNA virus 1 (LRV1) belongs to the To- clinical samples from 2014-2018 that were cryopre- tiviridae family, Leishmaniavirus genus, and infects served at Gorgas Memorial Institute's parasitology different Leishmania lineages. (cdc.gov)
  • RNA samples should be of high purity, recommended OD260/280 ~2.0 and OD260/230 ~1.8-2.2 based on spectrophotometric measurement (e.g. by Nanodrop). (lu.se)
  • Moreover, in vitro assays revealed that the decreased expression of lncRNA ANRIL could suppress the cell proliferation, migration and invasion HCC cells. (nih.gov)
  • RNA input amounts differ between assays. (lu.se)
  • The QIAseq Targeted RNA Panel (12) is intended for molecular biology applications. (qiagen.com)
  • QIAseq Targeted RNA Panels and Indices are intended for molecular biology applications. (qiagen.com)