Sequence gene expression profiling. Medical search. Frequent questions

Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
Annotating genomes with massive-scale RNA sequencing. (nature.com)
The gene ontology and pathway enrichment of DEGs were performed by DAVID and Kyoto Encyclopedia of Genes and Genomes online analyses, respectively. (hindawi.com)
Diversigen has optimized extraction methods for microbial mRNA, confirmed reproducible library preparation and sequencing approaches, and created a curated database with more than 190,000 genomes representing 31,000 species of microbes to allow profiling of gene expressions, pathways, and functional categories beyond what is possible with metagenomics or amplicon sequencing, the firm said. (genomeweb.com)
In the vast majority of eukaryotes, OXPHOS is operated by genes encoded by two genomes - most in the nuclear genome (nDNA) and 37 in the short circular mitochondrial genome (mtDNA). (biorxiv.org)
With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.com)
Sequence and annotate whole genomes of a variety of organisms using the Illumina MiSeq in the Genomics Lab . (rit.edu)
As the sequencing and gene annotation projects of entire genomes of many species are headed towards completion (see, e.g. [13] ), massive mapping efforts in biology are now focused on how the genes interact. (lu.se)
Sequencing Ebola and Marburg viruses genomes using microarrays. (cdc.gov)
As of August 10, 2000, draft sequence was available for 87% of the human genome (https://www.ncbi.nlm.nih.gov/genome/seq/), and at least 39 prokaryotic genomes, including those of more than a dozen human pathogens, had been completely sequenced https://www.tigr.org/tdb/mdb/mdbcomplete.html). (medscape.com)
Several independent high-throughput methods for differential gene expression (including SAGE and differential display) may enable function annotation of sequenced genomes [ 2 ] . (medscape.com)

We reasoned that gene expression profiling of COPD lungs could reveal previously unidentified disease pathways. (nih.gov)
But even so, gene-expression profiling can be enormously valuable in finding biomarkers, highlighting druggable targets, revealing the metabolic pathways important in a biological process, and identifying subsets of a population that might respond to a certain therapy or be more susceptible to a certain clinical outcome. (genengnews.com)
Diagnostic subsets of coexpressed genes reflected signaling activity, cross talk, and overlap of multiple mitogen-activated protein kinase (MAPK) pathways. (nih.gov)
What pathways are this gene/protein implicaed in? (cancerindex.org)
Thoracic aortic dissection (TAD) is a catastrophic disease worldwide, but the pathogenic genes and pathways are largely unclear. (hindawi.com)
This study aims at integrating two gene expression profile datasets and verifying hub genes and pathways involved in TAD as well as exploring potential molecular mechanisms. (hindawi.com)
Traditional bioinformatics methods including gene ontology (GO) and pathways enrichment analyses of DEGs combined protein-protein interaction (PPI) network and cytohubber calculating software as well as Molecular Complex Detection (MCODE) analysis were used to analyze the key gene and pathway. (hindawi.com)
The aim of this study was to identify the genes and pathways underlying the growth of the mouse sclera during postnatal development. (molvis.org)
Within the project using next generation sequencing technology and signal transduction pathway activity profiling technology, we have identified novel pathways and biomarkers implicated in cervical carcinogenesis. (europa.eu)
Polyphenol supplementation do not prevent the regulation of genes related to lipid metabolism in human adipose tissue during overfeeding, but impact the angiogenesis pathways. (bvsalud.org)
The project will identify key genes, pathways, and biological processes that are differentially regulated in response to hypoxia. (lu.se)

mRNA from the specimens was profiled using Agilent's Functional ID v2.0 array (Agilent, Santa Clara, CA) containing 23,720 sequences. (nih.gov)
These profiles measure mRNA, not protein, so further studies are needed to corroborate that any detected changes in gene expression actually have meaning in the life of the cell. (genengnews.com)
Using mRNA from total blood leukocytes, they found that a full one-quarter of the human genome exhibits changes in expression levels during the early stages of post-trauma (40-80 hours post-trauma). (genengnews.com)
Massive parallel signature sequencing (MPSS) is a procedure that is used to identify and quantify mRNA transcripts, resulting in data similar to serial analysis of gene expression (SAGE), although it employs a series of biochemical and sequencing steps that are substantially different. (wikipedia.org)
MPSS is a method for determining expression levels of mRNA by counting the number of individual mRNA molecules produced by each gene. (wikipedia.org)
MPSS allows mRNA transcripts to be identified through the generation of a 17-20 bp (base pair) signature sequence adjacent to the 3'-end of the 3'-most site of the designated restriction enzyme (commonly Sau3A or DpnII). (wikipedia.org)
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. (nature.com)
In the present study, we use mRNA microarray to acquire differential expression profiles in human TAD tissues and non-TAD tissues. (hindawi.com)
In general, mRNA levels of ECM and collagen genes have been found to be downregulated in both the adult mouse sclera [ 6 ] and cornea [ 7 ] when compared with samples from an earlier developmental stage. (molvis.org)
One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. (lirmm.fr)
The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate. (lirmm.fr)

Although high-throughput sequencing technologies have provided many diverse expressed genes, different expression profiles in TAD provided various results and no reliable results have been identified up to now [ 6 - 8 ]. (hindawi.com)
Intracellular amastigote protocols need further refinement, but we describe a first generation tool for high-throughput comparative molecular characterization of patients' isolates, based on the changing expression profiles of promastigotes during in vitro differentiation. (cambridge.org)
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)
A brief introduction to high throughput technologies for measuring and analyzing gene expression is given. (lu.se)
High-throughput methods for assessment of function are clearly required if this wealth of primary sequence information is to be used. (medscape.com)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)

Hara Levy, professor of physiology at the Human and Molecular Genetics Center of the Medical College of Wisconsin, studies cystic fibrosis (CF). Although CF is caused by mutations in the CF transmembrane conductance regulator gene, patients with identical genetic mutations in this gene can suffer variable levels of lung disease severity. (genengnews.com)
To identify novel molecular regulations, we performed a transcriptomic analysis based on the comparison of circulating MCL cells (n=77) versus MCL lymph nodes (n=107) together with RNA sequencing of malignant (n=8) versus normal B-cell (n=6) samples. (haematologica.org)
Molecular phenotyping through shallow 3′‐end RNA‐sequencing workflows is increasingly applied in the context of large‐scale chemical or genetic perturbation screens to study disease biology or support drug discovery. (researchgate.net)
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)
In fact, UMIs (unique molecular indices) entirely remove PCR bias in RNAseq counting (see figure Unmatched uniformity (>97% of assays are within 20% of median molecular tag counts) A 917-plex gene panel was used to prepare a library from 10 ng of NA12878 reference DNA. All assays were designed to be intra-exon, and are thus single copy on genomic DNA. This allows an estimation of the uniformity of amplicon performance in the library preparation step (e.g., every unique tag equals one captured copy). In terms of raw assay performance, 97.5% of assays are within 20% of mean/median molecular tag counts. For cataloged panels, any assay below 20% is redesigned and replaced. Molecular barcodes entirely remove this variation in RNAseq counting. "> Unmatched uniformity - 97% of assays are within 20% of median molecular tag counts ). (qiagen.com)
The purpose of this study was to develop a robust, standardized method for comparative expression profiling and molecular characterization of Leishmania donovani clinical isolates. (cambridge.org)
Transcriptome profiling reveals molecular players in early soybean - Sclerotinia sclerotiorum interaction. (usda.gov)
The market expansion is fueled by several factors such as the rise in adoption of sequencing platforms in clinical diagnostics , growth in genomics & enzymology-based research, and increase in investments in R&D. In addition, the significance potential of molecular biology and advancement in precision medicine are further augmenting market growth. (grandviewresearch.com)
Our master's or doctorate program in forest molecular genetics and biotechnology focuses on researching functional genomics, ecological genetics, gene expression profiling at the whole-genome scale, and genetic improvement of trees for sustainable biofuel. (mtu.edu)
More recently, next-gen sequencing has been rapidly moving into the clinical diagnostic arena and transforming the practice of molecular diagnostic testing. (aacc.org)
Dr. Shen, in your Perspective article you discuss the transformative effect of next-gen sequencing-based genetic testing, particularly exome and whole genome-based test on the molecular diagnostic practice. (aacc.org)
So, many changes brought by next-gen sequencing are transforming the molecular diagnostic practice. (aacc.org)
Articles are selected for AMD Clips if they discuss next-generation sequencing or other advanced molecular techniques applied to infectious disease diagnosis, surveillance, prevention, and control. (cdc.gov)
Other molecular approaches including gene expression profiles, metabolomics and studies of the microbiome offer promise for public health application in the next decade. (cdc.gov)
The molecular interactions of genes and gene products underlie fundamental questions of biology. (lu.se)
Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. (medscape.com)
By understanding the molecular details of this interaction, we can identify virulence-associated microbial genes and host-defense strategies and characterize the cues to which they respond and mechanisms by which they are regulated. (medscape.com)
The pace of gene discovery rapidly accelerates, but its potential for explaining life at the molecular level remains largely unrealized because our understanding of gene function lags increasingly far behind. (medscape.com)
His interests include Bordetella molecular pathogenesis and gene expression bioinformatics. (medscape.com)

Microarray technology and next-generation sequencing methods have enabled us to see all of the genes expressed by a given cell type at any particular time, or under a particular circumstance. (genengnews.com)
Then we downloaded another microarray dataset GSE52093 [ 9 ] and screened out the coexpression of differentially expressed genes (DEGs) between TAD patients and non-TAD patients. (hindawi.com)
Detecting Staphylococcus aureus Virulence and Resistance Genes - a Comparison of Whole Genome Sequencing and DNA Microarray Technology. (cdc.gov)

In November 2022, Broad's Genomics Platform sequenced its 500,000th whole human genome, a mere four years after sequencing its 100,000th. (broadinstitute.org)

Scope includes mutations and abnormal protein expression. (cancerindex.org)
Researchers have identified several hundred variants (also called mutations) in the ATM gene that cause ataxia-telangiectasia. (medlineplus.gov)
In a recent study published in the Nature Cardiovascular Research , researchers used single-cell sequencing methods to examine the cell-intrinsic effects of hematopoietic stem cells with somatic mutations that result in clonal hematopoiesis of indeterminate potential (CHIP), in circulating cells from heart failure patients. (news-medical.net)
Mutations in the epigenetic regulator genes deoxyribonucleic acid (DNA) methyltransferase 3 alpha (DNMT3A) and tet methylcytosine dioxygenase 2 (TET2), driven by clonal hematopoiesis have been implicated in the activation of inflammatory cytokines. (news-medical.net)
The inflammatory effect of clonal hematopoiesis driver mutations has also been observed at the single-cell level in the overexpression of inflammatory genes. (news-medical.net)
Single-cell ribonucleic acid sequencing (scRNA-seq) can be used to identify the cells with clonal hematopoiesis driver mutations in the DNMT3A gene to understand their role in heart failure. (news-medical.net)
An adapted bioinformatics pipeline was then used to identify the cells with specific coding sequence mutations in the DNMT3A gene. (news-medical.net)
The variant allele frequency of mutations identified previously from whole blood samples using targeted DNA sequencing was used to assess the ratio of mutant to wild-type cells and evaluate the efficiency of the MutDetect-seq method. (news-medical.net)
The researchers also investigated how the DNMT3A mutations influenced subsets of T cells, despite the fact that T cells exhibited a substantially lower number of upregulated genes. (news-medical.net)
The findings reported that altered gene expression profiles were identified in monocytes, NK cells, and CD4 + T cells containing DNMT3A mutations. (news-medical.net)
Accumulating evidence shows that tRNA expression and mutations are associated with various diseases such as neurological pathologies and cancer development3,4. (cdc.gov)
Characterization of novel Bruton's tyrosine kinase gene mutations in Central European patients with agammaglobulinemia. (lu.se)
Identification of Bruton tyrosine kinase mutations in 12 Chinese patients with X-linked agammaglobulinaemia by long PCR-direct sequencing. (lu.se)
Four novel and three recurrent mutations of the BTK gene and pathogenic effects of putative splice mutations. (lu.se)

The raw output is a list of 17-20 bp signature sequences, that can be annotated to the human genome for gene identification. (wikipedia.org)
Broad Genomics Platform sequences a whole human genome every four minutes. (broadinstitute.org)
Year 2011 is celebrated as the 10th anniversary since the human genome was first sequenced ( www.nature.com/natureconferences/hg10years/index.html ). (springer.com)

With the development of the gene expression profile, comparisons of differentially expressed genes that participate in the regulation of pathophysiological conditions in pathological tissue and normal tissue were available and convenient, and mRNAs gene expression profiles have been carried out in many diseases including TAD [ 6 ]. (hindawi.com)
A new gene regulation and labeling platform dubbed "Casilio" can simultaneously execute distinct functions at multiple areas of the genome at the same time, expanding researchers' ability to study gene function and chromosome structure, Jackson Laboratory (JAX) researchers report. (jax.org)
The higher expression of gremlin 1 and HIF1a genes after exposure to dragonfly larvae indicated an in vivo hypoxic reaction, while down-regulation of syndecan-2 may indicate impairment of angiogenesis. (biomedcentral.com)
When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata . (frontiersin.org)
Compared with red meat-diet-fed mice, fiber-diet-fed mice presented a shift in the gut microbiome toward increased production of butanoate, which was accompanied by up-regulation of microbiota- and AMP-activated protein kinase (AMPK)-dependent gene expression and decrease in serum concentrations of trimethylamine N -oxide (TMAO), triglyceride (TG) and glucose (GLU). (rsc.org)

The two expression profile datasets were integrated and we found out coexpression of differentially expressed genes (DEGs) using bioinformatics methods. (hindawi.com)
The integrated advanced bioinformatics methods may provide a way to solve the disadvantages and identify the hub genes involved in TAD. (hindawi.com)
Advances in genomics and bioinformatics, including whole genome sequencing are rapidly being integrated into public health surveillance and investigation of infectious disease outbreaks. (cdc.gov)
Moreover, utilizing advanced bioinformatics tools, the project will employ Gene Set Enrichment Analysis (GSEA) to discern the enrichment patterns of HIF-2α target upregulated genes within the obtained datasets. (lu.se)

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)
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 CORALL™ Total RNA-Seq V2 Library Prep kits from Lexogen enables easy and cost-efficient generation of UMI labelled, stranded libraries for whole transcriptome analysis using Illumina® next generation sequencing (NGS) platforms. (bioscience.co.uk)
Scientists from the Wellcome Trust Sanger Institute, University of Cambridge, and Illumina collaborated to use whole-genome sequencing to identify which isolates of methicillin-resistant Staphylococcus aureus (MRSA) were part of a hospital outbreak. (sanger.ac.uk)

dCas9 can be fused to protein tags or the effector domains of transcription factors (proteins that bind DNA in promoter regions and simultaneously bind other regulatory proteins via effector domains, which can activate or repress transcription and thereby affect gene expression) to develop customized DNA binding proteins. (jax.org)
A ubiquitously expressed sequence-specific transcriptional repressor that is normally the target of signaling by NOTCH PROTEINS. (harvard.edu)
Gene expression consists in the synthesis of proteins from the information encoded on DNA. (lirmm.fr)
Evaluation of phenotypic markers and expression of matrisome genes and proteins were evaluated by RNA-sequencing, mass spectrometry and immunohistochemistry. (lu.se)
COPD-derived AECs proliferated as healthy AECs with few differences in gene and protein expression while retaining increased expression of disease marker HLA-A. The AEC2 expressed basement membrane components and a complex set of interstitial ECM proteins. (lu.se)

Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. (broadinstitute.org)
However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. (broadinstitute.org)
Combining these new datasets with existing published gene expression and protein expression data have identified selected panels of novel biomarkers which have been evaluated on over 100 cervical cancer and pre-cancer cases using standard immunohistochemistry approaches. (europa.eu)

Single-cell RNA-sequencing (scRNA-seq) has revolutionized biomedical research by enabling the in-depth analysis of cell-to-cell heterogeneity of tissues with unprecedented resolution. (rsc.org)
In the present study, the researchers used Oxford Nanopore long-read sequencing to conduct scRNA-seq to detect DNMT3A mutant cells among circulating immune cells from patients with heart failure. (news-medical.net)

Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. (nature.com)

QIAseq Targeted RNA Panels have been developed as a Sample to Insight solution for quantitative gene expression profiling using RNAseq. (qiagen.com)
Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. (biorxiv.org)
Although such studies provided insights into the location of mtDNA promoters in the mentioned organisms, the techniques used were typically low throughput, were only semi quantitative, challenging to apply and require prior sequence knowledge. (biorxiv.org)
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)

Complete genomic sequences of microbial pathogens and hosts offer sophisticated new strategies for studying host-pathogen interactions. (medscape.com)

Interestingly, both TGF-beta1 and SERPINE2 have been identified as candidate genes in COPD genetic linkage and association studies. (nih.gov)
Genetic manipulations allowed analysis of changes in gene expression underlying pheromone signaling, cell cycle control, and polarized morphogenesis. (nih.gov)
Many diseases involve variations in gene expression rather than genetic sequence. (jax.org)
The wild plant species adapted to the Mongolian grassland environment may allow us to explore useful genes, as a source of unique genetic codes for crop improvement. (frontiersin.org)
For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
Next-generation sequencing has revolutionized the way researchers interrogate the genetic causes of rare single gene disorders. (aacc.org)

This progenitor later duplicated to generate CDYL and CDYL2, two autosomal genes found in all extant mammals. (syr.edu)

We show that the progenitor of this gene family arose de novo in the mammalian ancestor via domain accretion. (syr.edu)
Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. (biorxiv.org)
De novo mutation in the BTK gene of atypical X-linked agammaglobulinemia in a patient with recurrent pyoderma. (lu.se)

One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune . (nature.com)
Stochastic models of gene transcription with upstream drives: exact solution and sample path characterization. (crossref.org)
Our data reveal the differential expression landscape of 493 transcription factors and 682 lncRNAs and highlight specific expression clusters operating in HSCs. (lu.se)
EGFRIII changes the cell's internal signaling network, its uptake and use of nutrients, key elements of its gene-reading machinery known as transcription factors and its epigenetic landscape--the distribution of chemical tags that determines which parts of its genome are available for reading. (sciencedaily.com)
Most of the enhancers activated by EGFRvIII bore signature DNA sequences that are bound by dozens of transcription factors--regulators of gene expression--expressed at high levels in GBM. (sciencedaily.com)
This protein controls the expression and activity of yet another transcription factor, cMyc, which plays a central role in driving the aberrant metabolism and growth of GBM cells. (sciencedaily.com)
This pausing site correlated with the presence of a bacterial pausing sequence motif, yet the transcription pausing index varied quantitatively among the cell lines. (biorxiv.org)
This bi-genomic division is accompanied by profoundly different transcription regulatory system: whereas nDNA-encoded genes are transcribed individually by RNA polymerase 2 and the general nuclear transcription machinery, mtDNA transcription is long known to be regulated mainly by a dedicated RNA polymerase (POLRMT) and mtDNA-specific transcription factors (TFAM and TFB2) ( Shutt and Shadel 2010 ). (biorxiv.org)
However, as mtDNA transcription was mostly studied in vitro, little remains known about the mode and tempo of in vivo OXPHOS genes' transcription residing on the mtDNA. (biorxiv.org)
These obstacles interfered with comparative in-vivo investigation of mtDNA transcription in diverse conditions, and hampered expanding the study of mtDNA nascent transcripts to organisms lacking an mtDNA reference sequence. (biorxiv.org)
thus, genomewide transcription profiling seems particularly appropriate for the study of this process. (medscape.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)
With built-in UMIs and 384 UDIs for maximised sequencing output, and an all-in-one protocol, this technology allows for the complete and uniform transcript coverage from start to end, and flexible input requirements (1ng to 1 μg). (bioscience.co.uk)

Whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic Leptospira. (cdc.gov)

Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson's disease (n=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. (sens.org)
Current clinical methods to make links between related strains compare the pattern of bacterial susceptibility to a profile of antibiotics. (sanger.ac.uk)
The main emphasis is on supervised machine learning methods for classification and prediction of tumor gene expression profiles. (lu.se)
Furthermore, methods to rank the genes according to their importance for the classification are explored. (lu.se)
Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)
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)

Skeletal muscle is an inherently heterogenous tissue comprised primarily of myofibers, which are historically classified into three distinct fiber types in humans: one "slow" (type 1) and two "fast" (type 2A and type 2X), delineated by the expression of myosin heavy chain isoforms (MYHs). (researchgate.net)

The resulting cDNA was fragmented, labeled with biotin, and hybridized to a Mouse Gene 1.0 ST Array. (molvis.org)
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)

So if there are 50 copies of a specific transcript in the biological sample, these transcripts will be captured onto 50 different microbeads, each bead holding roughly 100,000 amplified copies of the specific signature sequence. (wikipedia.org)
The limitations and possibilities associated with expression profiling in intracellular amastigotes and promastigotes were assessed through a series of comparative experiments in which technical and biological parameters were scrutinized. (cambridge.org)
On the biological level, we demonstrate that gene expression levels fluctuate during in vitro development of both intracellular amastigotes and promastigotes. (cambridge.org)
We chose to use expression-curves rather than single, specific, time-point measurements to capture this biological variation. (cambridge.org)

Researchers around the globe are harnessing gene-expression profiling studies in a variety of clinical settings to prevent and treat a number of diseases. (genengnews.com)
Gene expression profiling is increasingly used in the field of infectious diseases for characterization of host, pathogen and the nature of their interaction. (cambridge.org)
Gene expression of eye diseases should be studied as early as postnatal weeks 1-2 to ensure that any changes in gene expression pattern during disease development are detected. (molvis.org)

The microbeads are then arrayed in a flow cell for sequencing and quantification. (wikipedia.org)
While these workflows enable accurate quantification of the most abundant genes, they are less effective for applications that requir. (researchgate.net)

In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences. (sens.org)
Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. (biorxiv.org)
Several genes (SDHD, SDHB, SDHC) that belong to the mitochondrial complex II have been identified as involved in the so-called pheochromocytoma-paraganglioma syndrome. (medscape.com)

To analyze the regulatory mechanism involved in the high growth potential of C. virgata , we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. (frontiersin.org)

Instead, they boost the expression of their target coding genes. (sciencedaily.com)

People with this disorder have variants in both copies of the ATM gene in each cell. (medlineplus.gov)
Instead of activating DNA repair, the altered ATM protein allows variants to accumulate in other genes, which may cause cells to grow and divide in an uncontrolled way. (medlineplus.gov)
In addition, ATM gene variants can allow cells to die inappropriately, particularly affecting cells in a part of the brain involved in coordinating movements (the cerebellum). (medlineplus.gov)
In particular, some studies have shown that cancers of the breast, stomach, bladder, pancreas, lung, and ovaries occur more frequently in ATM gene variant carriers than in people who do not carry these variants. (medlineplus.gov)
Additional research is needed to clarify which other types of cancer, if any, are associated with ATM gene variants. (medlineplus.gov)
Hall J. The Ataxia-telangiectasia mutated gene and breast cancer: gene expression profiles and sequence variants. (medlineplus.gov)
it has the possibility of detecting causal variants in genes that are not previously known to be associated with the disease. (aacc.org)

At the "Critical Assessment of Massive Data Analysis" conference held recently in Vienna, John Storey, from the Lewis-Sigler Institute for Integrative Genomics at Princeton University, gave a talk on dissecting the inflammatory complications in critically injured patients by within-patient gene-expression changes. (genengnews.com)

Immunohistochemistry confirmed expression of urokinase plasminogen activator (PLAU), urokinase plasminogen activator receptor (PLAUR), and thrombospondin (THBS1) by alveolar macrophages and airway epithelial cells. (nih.gov)
Results showed that the dietary interventions altered the microbiota composition of cecal digesta, microbiota-mediated metabolism, and the gene expression profile in intestinal epithelial cells. (rsc.org)

The longer tag sequence confers a higher specificity than the classical SAGE tag of 9-10 bp. (wikipedia.org)
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)

The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. (researchgate.net)
Pan-cancer RNA sequencing data revealed broad expression of the SAMMSON lncRNA in uveal melanoma (UM), the most common primary intraocular malignancy in adults. (researchgate.net)
The method has also been reported to perform well on problems similar to the classification of sequence data, such as the classification of text documents, that have a high-dimensional feature space and sparse data ( 16 ). (asm.org)
Next-gen sequencing has also brought many changes in the way we do assay validation in the lab, the way we do data analysis, data interpretation, and the way we report the finding to the referring physicians. (aacc.org)
The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. (usda.gov)
In a new study released today in New England Journal of Medicine , researchers demonstrate that whole-genome sequencing can provide clinically relevant data on bacterial transmission within a timescale that can influence infection control and patient management. (sanger.ac.uk)
Typically when data are presented, the fluor- escent intensity from the tissue is pseudo-colored red and the intensity from the reference green, and the logarithmic ratio of background corrected red and green intensities for each gene (spot) is subject to analysis (see Fig. 1 ). (lu.se)
Consolidating and exploring antibiotic resistance gene data resources. (cdc.gov)
DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. (medscape.com)
Genomic sequencing will provide the data needed to unravel the complexities of the host-pathogen interaction. (medscape.com)
Using available RNA sequencing data from previously published studies on intestinal organoids, the project will compare the gene expression profiles with newly generated RNA sequencing data from our lab's organoid cultures at hypoxia. (lu.se)
The GEO accession number for the sequencing data reported in this paper is GSE66550. (cdc.gov)

We describe isogenic colony sequencing (ICO-seq), a massively-parallel strategy to assess the gene expression profiles of large numbers of genetically distinct yeast colonies. (rsc.org)

The aim of this study was to acquire a better understanding of PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either PRRSV, porcine circovirus type 2 (PCV2), or swine influenza A virus (IAV). (usda.gov)
Evaluation of A Single-reaction Method for Whole Genome Sequencing of Influenza A Virus using Next Generation Sequencing. (cdc.gov)

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)

After several rounds of sequence determination, using hybridization of fluorescent labeled probes, a sequence signature of ~16-20 bp is determined from each bead. (wikipedia.org)
The sequence signatures are deciphered by the parallel identification of four bases by hybridization to fluorescently labeled encoders (Figure 5). (wikipedia.org)

It is "open ended" in the sense that the identity of the RNAs to be measured are not pre-determined as they are with gene expression microarrays. (wikipedia.org)
Microarrays are one such tool that allows for the study of expression of thousands of genes simultaneously. (lu.se)
In what follows we limit ourselves to the analysis of gene expression measurements obtained using microarrays with small spots of DNA fixed to glass slides. (lu.se)

The widely used CRISPR-Cas9 gene-editing technology has enabled researchers to alter genome sequence or gene expression with great precision, says JAX Assistant Professor Albert Cheng, Ph.D., first and co-corresponding author of a paper published in Cell Research . (jax.org)
For example, it can be fused to domains that activate or repress gene expression, allowing researchers to increase or decrease gene expression at will without changing the actual sequence. (jax.org)
Using technology developed in Ren's laboratory, the researchers began by profiling EGFRvIII's specific epigenetic activation of DNA sequences known as "enhancers. (sciencedaily.com)
The researchers show that as EGFRvIII alters the epigenetic landscape of activated enhancers, it also noticeably boosts the expression of SOX9 and FOXG1. (sciencedaily.com)
To find out if this potentially therapeutic effect might be induced by a drug, the researchers examined the genes whose expression is controlled by SOX9 and FOXG1. (sciencedaily.com)

It took me a long time to appreciate just how extensively population heterogeneity and other unmeasured sources of variation introduce unwanted and systematic biases into the statistical analysis of gene-expression studies," Dr. Storey noted. (genengnews.com)
This integrated analysis led to the discovery of microenvironment-dependent and tumor-specific secretion of interleukin-32 beta (IL32β), whose expression was confirmed in situ within MCL lymph nodes by multiplex immunohistochemistry. (haematologica.org)
Analysis of the profiles specified by two different MAPKs-Fus3p and Kss1p-revealed functional overlap of the filamentous growth and mating responses. (nih.gov)
Highly enriched cell populations were obtained and subjected to gene expression analysis. (ku.dk)
OraSure Technologies' Diversigen subsidiary has launched a service to provide metatranscriptomic sequencing and analysis of gut microbiome samples. (genomeweb.com)
Parts of the gene expression analysis market continue to develop in a somewhat predictable manner, whereas other segments are becoming increasingly complex and volatile. (kaloramainformation.com)
The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. (asm.org)
Total RNA was pooled for each group and time-point (1, 3, 6, and 14 DPI) to make 16 libraries, for analysis by Digital Gene Expression Tag Profiling (DGETP). (usda.gov)

Neofunctionalization is suggested by the rapid evolution of the CDY protein sequence. (syr.edu)
Thus, the CDY-related family offers an instructive example of how duplicated genes undergo functional diversification in both expression profile and protein sequence. (syr.edu)
This gene is a member of the protein-tyrosine kinase oncogene family. (cancerindex.org)
What does this gene/protein do? (cancerindex.org)
The new system, called Casilio, combines an altered version of CRISPR (CRISPR-dCas9) with the Pumilio RNA-binding protein system to enable much broader gene manipulation power. (jax.org)
The Pumilio RNA-binding protein system allows the design of a simple nucleotide code that recognizes an eight-nucleotide RNA sequence, called a PUF domain. (jax.org)
Immunoglobulin J Recombination Signal Sequence-Binding Protein" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)
This graph shows the total number of publications written about "Immunoglobulin J Recombination Signal Sequence-Binding Protein" by people in Harvard Catalyst Profiles by year, and whether "Immunoglobulin J Recombination Signal Sequence-Binding Protein" was a major or minor topic of these publication. (harvard.edu)
Below are the most recent publications written about "Immunoglobulin J Recombination Signal Sequence-Binding Protein" by people in Profiles. (harvard.edu)
The ATM gene provides instructions for making a protein that is located primarily in the nucleus of cells, where it helps control the rate at which cells grow and divide. (medlineplus.gov)
One of those genes turns out to be a protein named BRD4. (sciencedaily.com)
the tadpoles showed reduced expression of cα(E)-catenin , small muscle protein, dystrophin , and myosin light chain genes. (biomedcentral.com)

Genes involved in extracellular matrix synthesis/degradation and apoptosis were among the up-regulated genes, whereas genes that participate in antiinflammatory responses were down-regulated. (nih.gov)
Functional analyses indicated that some of the genes induced by dragonfly larvae caused an increase in laminins necessary for cell adhesion in the extracellular matrix. (biomedcentral.com)

The peroxisome proliferator- activated receptor gamma coactivator 1-alpha ( Ppargc1a ) gene was found to be involved in the networks generated using Ingenuity Pathway Studio (IPA) from the differentially expressed transcript cluster lists of week 2 versus 1, week 3 versus 2, week 6 versus 3, and week 8 versus 6. (molvis.org)

The best-aligned sequences were annotated with gene ontology groups. (frontiersin.org)

To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. (biorxiv.org)

Gene expression was related to forced expiratory flow between 25 and 75% of forced expiratory volume (FEF(25-75%) % predicted) revealing a signature gene set of 203 transcripts. (nih.gov)
The level of unique gene expression is represented by the count of transcripts present per million molecules, similar to SAGE output. (wikipedia.org)
Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. (sens.org)
Since genes are composed of a given alphabet (A, T, C, G) with fixed pairing properties A-T and C-G, probes can be constructed that attract gene transcripts extracted from cell tissues and cultures. (lu.se)

The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). (asm.org)
Not only could we distinguish different MRSA strains in the hospital, we were also able to rapidly characterise antibiotic resistance and toxin genes present in the clinical isolates. (sanger.ac.uk)
The team created a list of toxin genes to rapidly identify those present in the MRSA strains, which currently can only be identified with multiple assays in reference laboratories. (sanger.ac.uk)

The Wnt genes encode secreted glycoprotein ligands that regulate a wide range of developmental processes, including axis elongation and segmentation. (biomedcentral.com)

Genome-wide transcript profiling was used to monitor signal transduction during yeast pheromone response. (nih.gov)

0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of TAD. (hindawi.com)

6 ], the transforming growth factor beta 1 ( Tgfβ1 ) gene and several collagen genes were significantly downregulated in 8-week-old B6 mice scleras when compared with 3-week-old B6 mice scleras. (molvis.org)
In terms of clinical utility, next-gen sequencing will significantly improve the positive detection rate of tests, because many genes are tested simultaneously, as in the case of gene panel-based test, or all genes are interrogated in the case of whole exome or whole genome sequencing. (aacc.org)

As sequencing has become increasingly accurate and comprehensive, it can be used to answer a wide range of questions. (sanger.ac.uk)

This method combines the long-read sequences obtained using the Oxford Nanopore technology with short-read sequences from single-cell gene expression profiles. (news-medical.net)

What I mean by the transformative effect of next-gen sequencing in diagnostic laboratory is that next-gen sequencing has not just brought us a powerful new way of sequencing genes, most importantly, it has brought new approach on how we access patients, or the other way around, how patients can access the diagnostic testing, and how we perform tests and how we interpret the results. (aacc.org)

The results provide evidence that genes involved in tissue remodeling and repair are differentially regulated in the lungs of obstructed smokers and suggest that they are potential therapeutic targets. (nih.gov)
Here, we characterize the CDY-related mammalian gene family, focusing on three aspects of its evolution: gene copy number, tissue expression profile and amino acid sequence. (syr.edu)
Levels of gene expression are measured using a preparation of fluorescently labeled tissue RNA (copies of DNA), together with reference RNA labeled with a different fluorochrome, hybridized onto the slides. (lu.se)
The adaptive response to overfeeding is associated with profound modifications of gene expression in adipose tissue to support lipid storage and weight gain. (bvsalud.org)
The GO functions of these genes were mostly involved in lipid metabolism, followed by genes involved in adipose tissue remodeling and expansion. (bvsalud.org)
The project aims to elucidate the impact of oxygen levels on the HIF-2α pathway and its target genes in the context of intestinal stemness and tissue renewal. (lu.se)
It will extend to the identification and characterization of HIF-2α target genes, with a specific emphasis on their role in modulating the fundamental processes associated with intestinal stemness and tissue renewal. (lu.se)

The team constructed a list of all the MRSA genes that cause antibiotic resistance. (sanger.ac.uk)

Theories predict that the long-term survival of duplicated genes requires their functional diversification, which can be accomplished by either subfunctionalization (the partitioning of ancestral functions among duplicates) or neofunctionalization (the acquisition of novel function). (syr.edu)
The differences in gene expression profiles induced by the two predators suggest that there are functional differences between the altered tail tissues of the two groups of tadpoles. (biomedcentral.com)

We will combine our mRNAs expression profile (6 TAD tissues versus 6 non-TAD tissues) and GSE52093 downloaded from the Gene Expression Omnibus (GEO) database. (hindawi.com)

About 60% of GBM tumors are fueled by the mutation or rampant over-expression of EGFR, most often by the EGFRvIII mutant. (sciencedaily.com)
Mutation of the BTK gene and clinical feature of X-linked agammaglobulinemia in mainland China. (lu.se)

How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? (lu.se)

Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. (asm.org)

IL-17 induced NOTCH1 activation in oligodendrocyte progenitor cells enhances proliferation and inflammatory gene expression. (harvard.edu)

Nucleic acid cytometry using droplet microfluidics identifies and sorts single cells, virus, or free molecules based on specific "keyword" sequences. (rsc.org)

Anatomy20

Organisms10

Diseases22

Chemicals and Drugs48

Analytical, Diagnostic and Therapeutic Techniques and Equipment51

Phenomena and Processes78

Disciplines and Occupations6

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20221

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