Mrna sequence analysis rna. Medical search. Frequent questions

FastQC is a quality control tool for high-throughput sequence data (Babraham Institute) and is developed in Java. (wikipedia.org)
Kraken: A set of tools for quality control and analysis of high-throughput sequence data. (wikipedia.org)
The platform is made fully automated and capable of high-throughput sequencing by integrating the nanopipettes with the SU10 controller unit from Yokogawa Electric. (genomeweb.com)
Notably, these results were consistent with those obtained using high‑throughput sequencing. (spandidos-publications.com)
Here, we developed RNA-element selection assay (RESA), a method that selects RNA elements on the basis of their activity in vivo and uses high-throughput sequencing to provide a quantitative measurement of their regulatory functions at near-nucleotide resolution. (nih.gov)
The advent of high-throughput genotyping and gene expression profiling technologies has made it possible to use messenger RNA levels as quantitative traits in linkage studies. (columbia.edu)
Pmage is a technique that takes the best of Sage and high throughput DNA sequencing to obtain a global distribution of mRNA in any cell or tissue for a cost of about $1500 (?757) compared to about $10 000 for a Sage analysis, explained Seidman. (chemistryworld.com)
High-throughput genomic sequencing approaches have enormous potential with regard to unraveling complex heterogeneous phenotypes at the molecular level. (biomedcentral.com)
Although, the number of omic techniques is ever expanding, the most developed omics technologies are high throughput DNA sequencing, transcriptomics (focused on gene expression), epigenomics (focused on epigenetic regulation of gene expression), proteomics (focused on large sets of proteins, the proteome) and metabolomics (focused on large sets of metabolites, the metabolome). (who.int)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. (wikipedia.org)
One problem with identifying binding sites for splicing factors arises from the transient role of RNA in gene expression. (nih.gov)
The exon junction complex (EJC) deposited on spliced mRNAs, plays a central role in the post-transcriptional gene regulation and specific gene expression. (nature.com)
However, the comparative transcriptome analysis of two spinach accessions with different bolting times identified genome-wide gene expression profiling and large-scale discovery of flowering-related genes from vegetative and reproductive leaves [ 13 ]. (biomedcentral.com)
Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of transcription start sites at four different environmental conditions (limited in ethanol, limited in nitrogen, limited in glucose and limited in glucose under anaerobic conditions) using the Saccharomyces cerevisiae strain CEN.PK113-7D. (biorxiv.org)
To expand understanding of the role of snoRNAs in control of gene expression, in this study we tested the ability of artificial box C/D RNAs to affect the maturation of target pre-mRNA. (hindawi.com)
Gene expression is extensively regulated at the levels of mRNA stability, localization and translation. (nih.gov)
Several technologies exist to evaluate these changes including microarrays and serial analysis of gene expression (Sage). (chemistryworld.com)
To circumvent these challenges, Jon Seidman and colleagues at Harvard Medical School in Boston developed polony multiplex analysis of gene expression (Pmage). (chemistryworld.com)
This method shares many of the advantages of Sage over hybridisation-based approaches [such as DNA chips] but is a significant improvement over Sage,' said Kenneth Kinzler, professor of oncology and director of the Ludwig Center at Johns Hopkins University in Baltimore, MD. 'This may become the gold standard for gene expression analyses,' he said. (chemistryworld.com)
miRNAs are small noncoding RNAs that have broad regulatory functions on gene expression. (lu.se)
The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. (lu.se)
The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection. (lu.se)

To do this, messenger RNA (mRNA) is extracted from samples and sequenced. (idw-online.de)
NEW YORK - Researchers at the University of California, Santa Cruz have pioneered a method for repeatedly sampling messenger RNA (mRNA) from single cells without killing the cells in question. (genomeweb.com)
Where most scRNA-seq methods involve killing the cell from which messenger RNA is taken, the UCSC method leaves cells alive for further sampling, taking only between 1 and 5 percent of the cell's mRNA per sampling event. (genomeweb.com)
In order for these isolated cells to be useful, they need to be analyzed using droplet-based mRNA sequencing, also known as Drop-seq, which can measure messenger RNA expression in thousands of individual cells at once. (uclahealth.org)
The ability of the method to track changes in rare messenger RNA molecules (mRNAs) could ultimately make it indispensable as a diagnostic tool. (chemistryworld.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)

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)
Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. (biomedcentral.com)

Libraries from CRC tissue and adjacent normal tissues were analyzed on a single Genome Analyzer IIx lane (Illumina, USA) using 115 bp sequencing. (biomedcentral.com)
RSeQC analyzes diverse aspects of RNA-Seq experiments: sequence quality, sequencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. (wikipedia.org)
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. (dundee.ac.uk)
Interest in DNA testing is rising, because of developments in entire exome and genome sequencing methods, cost-effectiveness and faster results of the process when contrasted with genotyping based DNA microarray. (factmr.com)
The MZT marks the transfer of control of development from the mother to the zygote as maternal mRNAs are degraded, transcription from the zygotic genome begins, and embryonic development becomes dependent on zygotic gene products ( Tadros and Lipshitz, 2009 ). (elifesciences.org)
A total of six pairs of cancerous and adjacent healthy tissue were obtained from patients with HNSCC and genome‑wide transcriptional sequencing was performed. (spandidos-publications.com)
Using laser capture microdissection, epithelial cell-specific methylation signatures were characterized by whole-genome bisulfite sequencing of ileal and colonic samples at the time of surgery for NEC and after NEC had healed at reanastomosis ( n = 40). (biomedcentral.com)
Here we determined the epigenomic molecular phenotype of surgical NEC via genome-wide DNA methylation analysis. (biomedcentral.com)
Whole-genome sequencing (WGS) analyses of this tumor type are limited, and we therefore interrogated eight ATCs using WGS and RNA sequencing. (lu.se)
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning. (cdc.gov)
We have extensive whole genome and RNA sequencing data taken from whole samples of flies at three life stages: larva, pupa and adult. (lu.se)

We found that transfection of artificial box C/D snoRNA analogues directed to HSPA8 pre-mRNAs into human cells induced suppression of the target mRNA expression in a time- and dose-dependent manner. (hindawi.com)
Using such an approach, it was shown that introducing sequences complementary to a selected pre-mRNA into box C/D RNA structures allowed knockdown of the target mRNA [ 13 ]. (hindawi.com)
Notably, previous studies revealed that circRNAs participate in cancer pathogenesis by sponging miRNAs that target mRNA and circRNAs exhibit potential as predictive biomarkers and therapeutic targets for cancer treatment ( 5 , 6 ). (spandidos-publications.com)
It can directly bind to the 3'-untranslated region of the target mRNA through its seed sequence and inhibit the expression of the encoded protein at the post-transcriptional level [3]. (scirp.org)

To manipulate ribosome modifications and investigate how they alter translation of specific mRNAs we deplete known and putative modifying enzymes using siRNAs. (albany.edu)
We use ribosome profiling to monitor the effects of specific mutations to the eIF3 complex and investigate the features of the specific mRNAs most sensitive to these mutations. (vassar.edu)
The use of real-time quantitative RT-PCR to quantify specific mRNAs allows for more rapid testing, higher sensitivity, increased simplicity, and more accuracy. (medscape.com)

Analysis of the blue coral transcriptome revealed enrichment of genes involved in stress response, including heat-shock proteins and antioxidants, as well as genes participating in signal transduction and stimulus response. (nature.com)
Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. (biomedcentral.com)
Network analysis pinpointed several well-known flowering-related genes such as ELF , COL1 , FLT , and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. (biomedcentral.com)
This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. (biomedcentral.com)
Hundreds of genes were sequenced from each cell at each aspiration, and the genes sequenced showed high correlations from one sampling to the next, indicating that the small amount of mRNA withdrawn from each cell did significantly affect gene coverage. (genomeweb.com)
Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed genes (DEGs). (spandidos-publications.com)
Candidate target genes were identified through Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. (scirp.org)
Since the transcriptome includes the transcription of all mRNA in cells, except for abnormal mRNA degradation (like transcriptional decay), the transcriptome reflects the genes that are actively expressed at any given time. (capitalbiotechnology.com)
Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. (biomedcentral.com)
Differentially expressed genes (DEGs) for each treatment were identified with DESeq2 and uploaded to Ingenuity Pathway Analysis to identify and compare major changes in signaling pathways and cell functions. (cdc.gov)
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)
This will include co-expression network analyses to identify groups of genes that are expressed similarly and might belong to the same or linked gene regulatory networks. (lu.se)

Here we present an in-vitro method for screening RNA protein interactions that circumvents these problems. (nih.gov)
They are large complexes composed of RNA and protein molecules, and translate the mRNA sequence into a protein sequence. (albany.edu)
The subcellular distribution of an RNA quality control protein, the Ro autoantigen, is regulated by noncoding Y RNA binding. (albany.edu)
Here, using recombinant complex reconstitution and transcriptome-wide analysis, we showed that the EJC peripheral protein complexes ASAP and PSAP form distinct complexes with the EJC core and can confer to EJCs distinct alternative splicing regulatory activities. (nature.com)
Fertilization also leads to changes in mRNA translation and protein stability, which support a period of development driven off of maternal stockpiles. (elifesciences.org)
Circular RNAs (circRNAs) are closed, long, non-coding RNAs that are formed via direct reverse splicing of precursor mRNA that function by regulating RNA transcription and protein production, as well as sponging miRNAs ( 4 ). (spandidos-publications.com)
Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. (embl.de)
Anteroposterior patterning in Drosophila melanogaster is dependent on the sequence-specific RNA-binding protein Smaug, which binds to and regulates the translation of nanos (nos) mRNA. (embl.de)
The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug. (embl.de)
Finally, we used the versatile RESA platform to map candidate protein-RNA interactions in vivo (RESA-CLIP). (nih.gov)
In bacteria, a process called trans-translation has evolved, where a protein-RNA complex (smpB-tmRNA) mimicks the role of aminoacyl charged tRNA in the ribosomal A-site. (lu.se)
The ribosome then resumes protein synthesis guided by an mRNA-like portion of the tmRNA which ends with a stop codon and codes for a peptide sequence susceptible to proteolysis, thus allowing the bacteria to salvage stalled ribosomes and degrade ill-defined and potentially harmful protein products. (lu.se)
Author Manuscript and RNA repair protein AlkB-derived enzyme mixture was first used to remove methylations at the Watson-Crick face. (cdc.gov)
The effect of sequence variations within the coding region of the C1 inhibitor gene on disease expression and protein function in families with hereditary angio-oedema. (lu.se)

Most mRNAs contain information for enzymes, proteins that drive and regulate metabolism. (idw-online.de)
However, mass spectrometry analysis revealed that ribosomes within one organism, even within one single cell differ in posttranslational modifications and ribosome-associated proteins. (albany.edu)
SR-proteins constitute a family of RNA-binding proteins, which mainly regulate constitutive and alternative splicing. (forschung-sachsen-anhalt.de)
In addition to RNA recognition motifs (RRMs) the main characteristic of SR-proteins are disordered arginine and serine (RS) repeat regions. (forschung-sachsen-anhalt.de)
Our preliminary results suggest that SRSF1 (serine and arginine-rich splicing factor 1) and presumably other SR-proteins associate with non-coding (nc) RNAs, the highly structured 4.5SH RNA and Y RNAs. (forschung-sachsen-anhalt.de)
In contrast to Y RNAs the 4.5SH RNA is enriched in splicing speckles, suggesting that these ncRNAs modulate the association of SR-proteins within splicing speckles as well as other nuclear functions. (forschung-sachsen-anhalt.de)
We hypothesize that ncRNAs tether SR-proteins in splicing speckles, competing with their role in mRNA splicing. (forschung-sachsen-anhalt.de)
Hüttelmaier S.: Analysis of the oncogenic potential of SR-proteins by e.g. migration, invasion and proliferation assays. (forschung-sachsen-anhalt.de)
Box C/D RNAs are associated with four snoRNP core proteins: NOP56, NOP58, fibrillarin, and 15.5 kDa [ 5 - 7 ]. (hindawi.com)
Box C/D RNAs contain the following functional elements: boxes C and D, which are essential for snoRNA interaction with specific proteins, and a guide sequence that determines the nucleotide to be modified (Figure 1(a) ). (hindawi.com)
Spermatogenesis produces haploid sperm capable of penetrating the oocyte, whereas oogenesis produces differentiated oocytes that are stockpiled with maternal nutrients, proteins, and mRNAs, and have outer layers that protect the embryo and enable fertilization. (elifesciences.org)
Residues that compose the RNA-binding surface are conserved in a subgroup of SAM domain-containing proteins, suggesting that the function of the domain is conserved from yeast to humans. (embl.de)
The first study focused on inferring the in vitro binding specificity of RNA-binding proteins (RBPs). (columbia.edu)
The third study focused on post-transcriptional regulatory networks in yeast, by mapping the regulatory activity level of RNA binding proteins (RBPs) as a quantitative trait in so-called "aQTL" analysis. (columbia.edu)

Total RNA was extracted from tissues with TRIzol as per the manufacturer's protocol (Invitrogen, USA). (biomedcentral.com)
There is an important choice to be made when performing RNA-Seq - whether total RNA or mRNA sequencing should be used. (technologynetworks.com)
QIAseq FastSelect -rRNA Worm Kits are designed for quick, efficient removal of cytoplasmic and mitochondrial worm ribosomal RNA from total RNA during NGS RNA library preparation. (qiagen.com)
Prior to RNA heat fragmentation (which is optional and dependent upon the library preparation kit and sample type), QIAseq FastSelect removal reagent is directly combined with total RNA and the library preparation-specific buffers. (qiagen.com)
There is no need to perform any type of enrichment on the total RNA samples. (qiagen.com)
Total RNA is converted to double-stranded complementary DNA molecules, which are cleaved to form tags. (chemistryworld.com)
Next, mRNA libraries were prepared from total RNA from lysed cells and subjected to RNAseq on an Illumina Novaseq. (cdc.gov)
Our RNA service includes mRNA and total RNA library preparation and sequencing on Illumina platforms. (lu.se)
TaKaRa SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian for low input and poor quality samples. (lu.se)

The NanoString immune-oncology RNA targets panel was used to determine the transcriptional profile of active fibrotic areas within orbital sections. (frontiersin.org)
highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. (biomedcentral.com)
The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. (embl.de)
However, decoding functional RNA-regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. (nih.gov)
Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)

The focus of this meeting will be on structure, function, specificity of RNA editing and modifications and their respective enzymes, as well as the evolution and biological role of editing and modification in health and disease. (grc.org)
We show here that the SAM domain of Saccharomyces cerevisiae Vts1 binds RNA with the same specificity as Smaug and that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. (embl.de)
We first analyzed a recent compendium of in vivo mRNA binding data to model the sequence specificity of 45 yeast RBPs in the form of a position- specific affinity matrix (PSAM). (columbia.edu)

One thousand seven hundred and sixteenth differentially expressed mRNAs and 311 differentially expressed lncRNAs were screened out. (biomedcentral.com)

We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). (dundee.ac.uk)
rRNAs and snRNAs are the main natural targets of 2′-O-methylation that is mediated by box C/D RNAs. (hindawi.com)
The aim of our study was to determine the molecular phenotype of NEC via transcriptomic and epithelial cell-specific epigenomic analysis, with a specific focus on DNA methylation. (biomedcentral.com)

The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. (wikipedia.org)
This can fundamentally be credited to the government support through funds for genomics research, growing prevalence of target diseases, advancements in RNA-Seq products, rising research on inherited rare diseases and cancer, and therefore the solid presence of key players like Thermo Fisher (US), Illumina (US), and Agilent Technologies (US). (factmr.com)
QIAseq Stranded RNA Library Kits utilize unique dual indexing (UDIs) which enables multiplexing of up to 384 samples per flow cell lane on Illumina NGS instruments and mitigates index hopping on Illumina NovaSeq and Illumina patterned flow cells. (qiagen.com)
Demultiplexed data files generated from the Illumina sequencing run. (lu.se)

mRNA vaccine quality analysis using direct RNA sequencing. (springernature.com)

Small nucleolar RNAs (snoRNA) are commonly known to be involved in the processing of precursor ribosomal RNA (pre-rRNA) and small nuclear RNAs (snRNAs). (hindawi.com)

The recent focus of the lab has been on applying deep learning methods to detect and differentiate aggressive from indolent prostate cancers on MRI using the pathology information (both labels and the image content), work that was recently published in Medical Physics and Medical Image Analysis Journals. (stanford.edu)
Prior to joining Stanford, Dr. Rusu was a Lead Engineer and Medical Image Analysis Scientist at GE Global Research Niskayuna NY where she was involved in the development of analytic methods to characterize biological samples in microscopy images and pathologic conditions in MRI or CT. (stanford.edu)
But these methods are limited by their inability to detect low abundance RNAs. (chemistryworld.com)
The tool significantly reduces the time and resources required to perform degradome analysis, in some cases providing more than two orders of magnitude speed-up over current methods. (uea.ac.uk)
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)
One of the methods that does seem to work well is TargetScan, which relies on both pairing of seed sequences (a subset of the 18-23 bp that make up a miRNA) and phylogenetic conservation of sites. (lu.se)

A real-time reverse transcription PCR, targeting 2 alternatively spliced mRNAs, was developed. (cdc.gov)

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)

This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. (medscape.com)
Because of the complexity of the data sets generated by microarray experiments, the use of data-analysis software is essential. (medscape.com)

Transcriptome-wide RNA-seq studies revealed that ASAP and PSAP complexes regulate distinct alternative splicing events both in EJC-independent and EJC-dependent manner. (nature.com)
Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. (dundee.ac.uk)

Thus, further investigations into the specific molecular mechanisms underlying circRNA/miRNA/mRNA regulation are required to aid discovery of effective therapeutic targets. (spandidos-publications.com)
Reverse transcriptase (RT) PCR is PCR performed on RNA targets. (medscape.com)

b) Base-pairing interactions between an artificial box C/D RNA and target RNAs. (hindawi.com)
The present study aimed to screen and explore the key circRNA/microRNA (miRNA or miR)/mRNA interactions in head and neck squamous cell carcinoma (HNSCC) using bioinformatics. (spandidos-publications.com)
The resulting mRNA fragments, or degradome, provide evidence for these interactions, and thus degradome analysis has become an important tool for sRNA target prediction. (uea.ac.uk)
We will apply this approach to a non-model sparrow study system to answer questions about how hybridization can disrupt evolved miRNA-mRNA interactions, leading to insights about the formation of new species. (lu.se)

The current study aimed to evaluate the expression pattern of lncRNAs and messenger RNAs (mRNAs). (biomedcentral.com)
In addition, 1448 lncRNA-mRNA co-expression pairs were screened out from 940,905 candidate lncRNA-mRNA pairs. (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)
RNA-sequence analysis revealed that curcumin intake affected hepatic lipid metabolism via the peroxisome proliferator-activated receptor (PPAR) pathway, especially PPARα activation, resulting in increased Apoa2 mRNA expression. (elifesciences.org)
We used the collection of 15 sequence motifs with the associated mRNA region combinations that we obtained in our first study together with mRNA expression data to estimate RBP activities across yeast segregants. (columbia.edu)
Changes in the expression of mRNAs often accompany the progression of a tissue from a healthy to a diseased state. (chemistryworld.com)
Using RNA sequencing (RNA-seq) data from primary and xenograft SCLC samples, we identified seizure-related homolog 6 (SEZ6) as a surface-expressed SCLC target with broad expression in SCLC and minimal normal tissue expression by both RNA-seq and IHC. (aacrjournals.org)
Because the locations of the probes are known, the intensity and pattern of the labeled mRNA can be used to measure the expression of the targeted gene. (medscape.com)
Normal C1 inhibitor mRNA expression level in type I hereditary angioedema patients: newly found C1 inhibitor gene mutations. (lu.se)

The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. (biomedcentral.com)
Bioinformatics support in RIP/CLIP-studies and RNA-sequencing (splicing regulation). (forschung-sachsen-anhalt.de)
Our analysis supplies a set of high quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation. (biorxiv.org)
Circular RNAs (circRNAs) are molecular sponges that are involved in regulation of multiple types of cancer. (spandidos-publications.com)

Now we have a method that gives a very clear frequency distribution of mRNA molecules in a cell,' he said. (chemistryworld.com)
During translation, mRNA molecules are incidentally damaged, leaving the ribosome unable to reach or recognize the stop codon and thus stalled with mRNA and a potentially harmful polypeptide product attached to tRNA in the ribosomal P-site. (lu.se)

Gene enrichment analysis was demonstrated using DAVID 6.8 tool. (biomedcentral.com)
Gene enrichment analysis revealed that these lncRNA-related mRNAs are associated with cell adhesion, collagen adhesion, cell differentiation, and mainly enriched in ECM-receptor interaction and PI3K-Akt signaling pathways. (biomedcentral.com)

We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. (dundee.ac.uk)

RNA input amounts differ between assays. (lu.se)

Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. (mdpi.com)
It was previously shown that transcription of a gene in eukaryotic cells is not always initiated from the same nucleotide, but that it can be initiated from a range of positions in the core promoter region, with an individual, sequence-influenced pattern for each gene ( 3 - 6 ). (biorxiv.org)
To develop a qualitative reverse transcription PCR to detect spliced mRNA from HBoV1 and to determine whether HBoV1 mRNA correlated better with RTIs than did HBoV1 DNA, we used samples from HBoV1 DNA-positive children, with and without RTIs, to evaluate the test. (cdc.gov)
The main objectives of this study were to develop a qualitative reverse transcription PCR (RT-PCR) detecting spliced mRNA from HBoV1 and to clarify whether HBoV1 mRNA detection may correlate better than DNA detection with RTIs in children. (cdc.gov)
Reverse transcription is the synthesis of a complementary DNA sequence from an RNA template using reverse transcriptase, which is an RNA-dependent DNA polymerase. (medscape.com)

Moreover, GenapSys, a U.S. - based designer of mRNA sequencing advancements for applied genomic testing, presented a GENIUS sequencer, which can sequence DNA anywhere. (factmr.com)
With the development of next-generation sequencing (NGS), research has focused on comprehensive genomic analysis based on tumor molecular features, such as somatic mutations and copy number variation. (spandidos-publications.com)

In plants, this typically results in mRNA cleavage and subsequent degradation of the mRNA. (uea.ac.uk)
Freeze and thaw samples as few times as possible and work with the RNA on ice to avoid degradation. (lu.se)

Removing highly expressed, but biologically unimportant RNA transcripts makes NGS more efficient and enables higher sample throughput with higher sensitivity. (qiagen.com)
However, a number of snoRNA-like transcripts do not have guide sequences that are complementary to rRNA or snRNA, so they have unknown functions and are called "orphan snoRNAs" [ 8 , 9 ]. (hindawi.com)

The mRNA Sequencing market is highly fragmented, with the existence of many large-scale players available in global markets, and various small-scale participants in regional markets. (factmr.com)
We recommend using QIAseq Stranded RNA Library Kits for robust strand-specific RNA-seq library preparation for high-quality and highly fragmented (FFPE) RNA. (qiagen.com)

Researchers using RNA-seq for whole transcriptome analysis can use QIAseq FastSelect -rRNA Worm Kits to remove all annotated rRNAs in RefSeq and Ensembl for Caenorhabditis elegans (worm). (qiagen.com)

Inasmuch as artificial box C/D RNAs decreased viability of transfected human cells, we propose that natural snoRNAs as well as their artificial analogues can influence the maturation of complementary pre-mRNA and can be effective regulators of vital cellular processes. (hindawi.com)
The nucleotides to be complementary to target nucleotides are shown as C . RNA7D* and RNA8D* were constructed by changing the CUGA sequence in both box D and D′ to AAAA. (hindawi.com)
Bioinformatics analysis revealed that some of these orphan RNAs were complementary to pre-mRNAs or mature mRNAs [ 10 ]. (hindawi.com)
MBII-52 box C/D snoRNA containing a guide sequence complementary to the serotonin receptor 2C pre-mRNA was reported to take part in controlling the posttranscriptional modification of the target pre-mRNA (conversion A to I) [ 11 ]. (hindawi.com)
It was also shown that HBII-52 snoRNA could regulate alternative splicing of the complementary pre-mRNA [ 12 ]. (hindawi.com)

RNA sequencing (RNA-Seq) is a powerful and comprehensive method for analyzing the cellular transcriptome, enabling qualitative and quantitative examination of multiple types of RNA. (technologynetworks.com)
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)

Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen. (albany.edu)
Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity. (albany.edu)
In study by Ono and coworkers, such an antisense element was placed into HBII-180C box C/D RNA instead of the structural element referred to as the M box [ 13 ]. (hindawi.com)
Lindahl, M 2010, ' tmRNA to the rescue Structural motives for the salvage of stalled ribosomes ', RNA Biology , vol. 7, nr. 5, s. 577-581. (lu.se)

In addition, a previous study demonstrated that circRNA/miRNA/mRNA networks are involved in the development and progression of multiple types of malignancy ( 7 ). (spandidos-publications.com)
miRNA is a non-coded RNA with a length of 19 - 25 bases. (scirp.org)

abstract = "Small RNAs (sRNAs) are short, non-coding RNAs that play critical roles in many important biological pathways. (uea.ac.uk)

Recently snoRNAs are predicted to regulate posttranscriptional modifications of pre-mRNA. (hindawi.com)

The primary role of most splicing factors is to bind pre-mRNA co-transcriptionally and participate in the extremely rapid process of splice site selection and catalysis. (nih.gov)
SRSF1 is upregulated in a variety of cancers, promoting and inhibiting pro-proliferative versus anti-apoptotic mRNA splice variants, respectively. (forschung-sachsen-anhalt.de)

We prepared a total of n = 40 bisulfite sequencing libraries from individual tissue samples following laser capture microdissection of intestinal epithelial cells in each case. (biomedcentral.com)

Long non-coding RNAs (lncRNAs ) are widely involved in the pathogenesis of cancers. (biomedcentral.com)

RNA sequencing was also performed to determine the transcriptomic profile of these samples, and a comparison was made to the methylome data. (biomedcentral.com)

Initially, DNA is taken from the clinical specimen, as well as certain sequence-specific oligonucleotide primers, thermostable DNA polymerase, nucleotides, and buffer. (medscape.com)

Bley N.: Immunofluorescence, FRAP analyses and fluorescence in situ hybridization (FISH) experiments. (forschung-sachsen-anhalt.de)
Exhaustive mutation scanning by fluorescence-assisted mismatch analysis discloses new genotype-phenotype correlations in angiodema. (lu.se)

8] when using sequence analysis of human colorectal cells. (scirp.org)

Synthetic promoters are designed by combining core promoters with different upstream regulatory sequences. (biorxiv.org)

RNA-Seq is a technique that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. (wikipedia.org)
Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. (biomedcentral.com)

By comparing the mRNAs sensitive to both DDKK and Degron mutations to those mRNAs uniquely sensitive to the Degron mutation, we hope to disentangle the contributions of eIF3i and eIF3g from those of eIF3a, eIF3b, and eIF3c. (vassar.edu)

Assembly of the ribosome on a specific mRNA during initiation is an important step for regulating translation. (vassar.edu)
To investigate the role of eIF3 in translation initiation, we employ ribosome profiling, which enables us to learn the position of each translating ribosome on every mRNA in living cells. (vassar.edu)

The raw sequencing data is secondary analyzed, and the 6 pairs of CRC tissues were divided into two groups (group 1 and group 2, corresponding to clinical stage II and III, Table S 1 ) based on their clinical stages. (biomedcentral.com)
Quality assessment of raw data is the first step of the bioinformatics pipeline of RNA-Seq. (wikipedia.org)
Often, is necessary to filter data, removing low quality sequences or bases (trimming), adapters, contaminations, overrepresented sequences or correcting errors to assure a coherent final result. (wikipedia.org)
mRIN - Assessing mRNA integrity directly from RNA-Seq data. (wikipedia.org)
NGSQC: cross-platform quality analysis pipeline for deep sequencing data. (wikipedia.org)
NGS QC Toolkit A toolkit for the quality control (QC) of next generation sequencing (NGS) data. (wikipedia.org)
It also includes few other tools, which are helpful in NGS data quality control and analysis. (wikipedia.org)
PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. (wikipedia.org)
It is particular designed for 454/Roche data, but can also be used for other types of sequence. (wikipedia.org)
QC-Chain is a package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. (wikipedia.org)
QC3 a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling. (wikipedia.org)
The resulting RNA-seq data showed high alignment rates of approximately 80 percent with two control tissue samples. (genomeweb.com)
The Gordon Research Seminar on RNA Editing is a unique forum for graduate students, post-docs, and other scientists with comparable levels of experience and education to present and exchange new data and cutting edge ideas. (grc.org)
Analyze RNA-seq data with ease using the GeneGlobe-integrated RNA-seq Analysis Portal - an intuitive, web-based data analysis solution created for biologists and included with this QIAseq Kit. (qiagen.com)
The data for these analyses comes from segregating populations of Saccharomyces cerevisiae (baker's yeast) as well as Caenorhabditis elegans (roundworm). (columbia.edu)
Our data support the hypothesis that HBoV1 may cause RTIs, and we propose that HBoV1 mRNA could be used with benefit, instead of HBoV1 DNA, as a diagnostic target. (cdc.gov)
As a result, existing degradome analysis tools are unable to process the volume of data being produced without imposing huge resource and time requirements. (uea.ac.uk)
CTG uses secure LSENS servers hosted by LUNARC for internal data management and analysis. (lu.se)
After sequencing, data will be kept by CTG for 3 months and subsequently deleted . (lu.se)
Lack of detail in population-level data impedes analysis of SARS-CoV-2 variants of concern and clinical outcomes. (cdc.gov)
Given the sensitivity of -omic analyses, low- dose adverse effects could also be observed and distinguished from high dose phenomena, and if exposures were accurately assessed, dose-response data could be incorporated into risk assessments. (who.int)
Several commercial and public data-analysis tools have been developed for this purpose. (medscape.com)
The GEO accession number for the sequencing data reported in this paper is GSE66550. (cdc.gov)
However, most GEP studies have typically been performed on whole tissue samples, containing varying degrees of tumor cell content, which results in uncertainties in data analysis. (lu.se)

Metatranscriptome assembly yielded 90,817 sequences of which 71% (64,610) could be annotated by comparison to public databases. (nature.com)
So-called metatranscriptome analyses are an attractive way to find out what metabolic processes are going on in a complex microbial community. (idw-online.de)

We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. (nih.gov)

One of the more predominant mutational signatures was intimately coupled to the activity of Apolipoprotein B mRNA-editing enzyme, the catalytic polypeptide-like (APOBEC) family of cytidine deaminases implied in kataegis, a focal hypermutation phenotype, which was observed in 4/8 (50%) cases. (lu.se)

Interestingly, EJCs are not loaded equally across all exon junctions of a mRNA. (nature.com)
The artificial box C/D RNA directed to the branch point adenosine of the second intron, as well as the analogue directed to the last nucleotide of the second exon of the HSPA8 pre-mRNA caused the most prominent influence on the level of HSPA8 mRNAs. (hindawi.com)

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)

Here, we determined the effect of Jiyuan oridonin A (JOA), an ent -kaurene diterpenoid compound, on the differentiation blockade in imatinib-sensitive, particularly, imatinib-resistant CML cells with BCR-ABL-T315I mutation by cell proliferation assay, apoptosis analysis, cell differentiation analysis, cell cycle analysis and colony formation assay. (jcancer.org)
The method, which was recently published in the journal PLoS One , relies on automated nanopipetting from slide-mounted, intact tissue and mRNA capture using a just-launched magnetic mRNA purification and sequencing library preparation platform from nanoparticle assay developer Nvigen. (genomeweb.com)

To better understand the molecular mechanisms underlying its biology and ecology, we generated a reference transcriptome for H. coerulea using next-generation sequencing. (nature.com)
We also investigated the possible molecular mechanism by mRNA sequencing, qRT-PCR and Western blotting. (jcancer.org)
A molecular regulatory network consisting of three circRNAs, seven miRNAs and seven mRNAs was constructed, resulting in identification of two signaling axes, hsa_circ_0035431/hsa‑miR‑940/fucosyltransferase 6 (FUT6) and hsa_circ_0035431/hsa‑miR‑940/cingulin‑like 1 (CGNL1). (spandidos-publications.com)
C.P. tion stage, why much more detailed molecular analysis is contributed to the design of the study, discussions on statistical analysis of called for [2]. (lu.se)
The recommendation is to freeze and store a portion of suspected sarcomas or poorly differentiated malignant lesions for molecular analysis. (medscape.com)

Proteomic analysis of ribosomes: translational control of mRNA populations by glycogen synthase GYS1. (albany.edu)

Transcriptome in vivo analysis (TIVA), for example, enters cell membranes via a cell-penetrating peptide. (genomeweb.com)

Pre-mRNA is a labile species with a steady state level that is three orders of magnitude less abundant than mRNA. (nih.gov)

According to the latest research by Fact.MR, the mRNA Sequencing market is set to witness steady growth during 2021-2031. (factmr.com)

Uppercase letters in the target pre-mRNA sequences correspond to exons, and small letters indicate the intron sequences. (hindawi.com)

A number of RNA-Seq quality control analyses summarized in FastQC and MultiQC reports. (lu.se)

Even so, with the continuing advances in sequencing technologies, not only are larger and more complex genomes being sequenced, but also degradome and associated datasets are growing both in number and read count. (uea.ac.uk)

The challenge lies in the instability of mRNA and the relatively small amounts found on washed linen. (idw-online.de)
QIAseq FastSelect -rRNA Worm Kits ensure consistently high performance with RNA amounts ranging from as little as 1 ng up to 1 μg. (qiagen.com)
Additionally, small amounts of input RNA are required. (medscape.com)

cloned and sequenced a cDNA copy of the bovine prePOMC mRNA. (wikigenes.org)

In the proof-of-concept study, Pourmand's group aspirated 22 cells within a breast cancer tissue slice and selectively captured the mRNA using Nvigen's proprietary antibody-coated magnetic nanoparticles. (genomeweb.com)

Depending on rRNA sequence homology, QIAseq FastSelect −rRNA Worm will work on additional worm species (dependent upon target rRNA sequence homology with C. elegans ). (qiagen.com)
QIAseq FastSelect can be used with RNA from fresh samples from many species of worm (dependent upon target rRNA sequence homology with C. elegans ), and delivers reliable rRNA removal and high reproducibility in downstream applications. (qiagen.com)

Anatomy15

Organisms13

Chemicals and Drugs100

Analytical, Diagnostic and Therapeutic Techniques and Equipment29

Phenomena and Processes99

Disciplines and Occupations3

Information Science9

Health Care3

High-throughput10

Gene expression13

Messenger RNA6

LncRNA-mRNA co-expression network2

Genome11

Target mRNA4

Specific mRNAs3

Genes13

Protein14

Proteins14

Total RNA9

Transcriptional6

Specificity3

Differentially expressed1

Methylation3

Illumina4

Vaccine quality analysis1

Processing of precursor1

Methods7

Alternatively spliced1

Ribosomal RNA1

Microarray2

Transcriptome-wide2

Targets2

Interactions4

Expression9

Regulation4

Molecules2

Enrichment2

Nanopore1

Assays1

Transcription5

Genomic2

Degradation2

Transcripts2

Highly fragmented2

Whole transcriptome1

Complementary5

Quantitative3

Structural4

MiRNA2

Abstract1

Regulate1

Splice2

Libraries1

Pathogenesis1

Transcriptomic1

Nucleotides1

Fluorescence2

Colorectal1

Regulatory sequences1

Transcriptomics2

Mutations1

Ribosome2

Data24

Metatranscriptome2

Stability1

Enzyme1

Exon2

Bioinformatic1

Assay2

Molecular5

Translational1

Vivo1

Abundant1

20211

Intron1

MultiQC1

Genomes1

Amounts3

CDNA1

Tissue1

RRNA2