Specific sequence analysis dna. Medical search. Frequent questions

Modified comparative genomic analysis was used to find the best specific target sequence to detect S. epidermidis . (ajmb.org)
To determine the detection limit and analytical specificity, pure genomic DNA of 18 bacteria include 12 standard strains (one S. epidermidis and 11 non- S. epidermidis ) and six clinical isolates (five S. epidermidis and one non- S. epidermidis ) were used. (ajmb.org)
The detection limit of Se400-PCR was 10 fg , equal to about 4 copies of S. epidermidis genomic DNA/μl . (ajmb.org)
Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. (mpg.de)
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. (mpg.de)
Ligation detection reaction-TaqMan procedure for single nucleotide polymorphism detection on genomic DNA. (mpg.de)
Refinement of single-nucleotide polymorphism genotyping methods on human genomic DNA: amplifluor allele-specific polymerase chain reaction versus ligation detection reaction-TaqMan. (mpg.de)
To identify the mutation responsible for renal disease, we sequenced genomic DNA from an affected animal using the Applied Biosystems SOLiD sequencing platform. (nih.gov)
The disorders are characterized by a defect in DNA repair mechanisms or genomic stability, and patients with these disorders show increased predisposition to cancer. (medscape.com)
DNMT1 preserves the methyltransferase by binding to hemi-methylated CpG sites and methylates the cytosine on the newly synthesized strand after DNA replication, whereas DNMT3a/DNMT3b are required for the de novo genomic methylation of DNA ( 15 ). (spandidos-publications.com)
Genomic and transcriptomic sequencing analyses were performed with phenotypic validation to investigate its adaptation in SARS-CoV-2 infected environment. (frontiersin.org)
Genomic characterization predicted specific genomic islands highly associated with virulence, transcriptional regulation, and DNA restriction-modification systems. (frontiersin.org)
Three specific biomolecular techniques are addressed: polymerase chain reaction, microarray comparative genomic hybridization, and whole-genome sequencing. (umd.edu)
For microarray, novel pan-genomic design and analysis methods are presented for the characterization of unknown microbial isolates. (umd.edu)
Reagents capable of cutting DNA are applied within these fields as probes for DNA structure and function, with the ultimate aim being the design of target-specific-customised endonucleases-capable of modifying genomic DNA. (dcu.ie)
Many compounds developed in this work constitute a series of novel anticancer leads capable of intracellular DNA oxidation leading to genomic double strand breaks. (dcu.ie)
We designed a project of forensic genetics, to identify the human soft tissues, based on the quantification of DNA methylation at specific genomic regions of different human tissues. (slu.se)
In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. (umassmed.edu)
These two phage clones specifically hybridized to L. helveticus 481 total genomic DNA but not to DNA from strains that did not produce helveticin J or strains producing unrelated bacteriocins. (ncsu.edu)
PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. (biorxiv.org)
Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. (lu.se)
Each archetype was characterised by specific clinical, genomic, and microenvironmental features. (who.int)

Our study demonstrates the speed and utility of whole genome sequencing coupled with low resolution meiotic mapping as a means of identifying causative mutations induced by ENU. (nih.gov)
feed matrix to subsequently perform a whole-genome-sequencing. (pulsus.com)
If all goes as planned, in the third quarter of 2011, OpGen will launch the system for whole-genome sequence assembly and finishing for research on larger organisms, such as plants and animals, including humans, CEO Doug White told GenomeWeb Daily News . (genomeweb.com)
OpGen's Optical Mapping Technology is a method of deciphering a genome's architecture by creating high-resolution, ordered, whole-genome restriction maps from single DNA molecules. (genomeweb.com)
We make a fingerprint of the DNA, of the whole genome, that we can then put into our database and we can compare it with other isolates. (genomeweb.com)
Applications for the technology include strain typing and whole-genome sequence assembly. (genomeweb.com)
For whole-genome sequence assembly and finishing, the Optical Mapping System is complementary to existing second- and forthcoming third-generation sequencing technologies, he said, in that it can provide a complete genome scaffold for contig alignment and orientation. (genomeweb.com)
This dissertation presents novel computational methods that unlock the potential of these diagnostics by efficiently analyzing whole-genome DNA sequences. (umd.edu)
Finally, multiple methods are presented for the validation of whole-genome sequence assemblies, which are capable of identifying assembly errors in even finished genomes. (umd.edu)
To address this aim we have designed the lungNENomics study, an international cohort of over 250 cases of pulmonary carcinoids, with clinical data and central pathology review, as well as whole-genome sequencing, RNA sequencing, DNA methylation array, and digital spatial profiling data. (who.int)

Annotating genomes with massive-scale RNA sequencing. (nature.com)
The 400 bp sequence of S. epidermidis ATCC 14990 was identified as the most specific sequence (Se400), having a 100% sequence similarity to S. epidermidis genomes but not with other bacteria. (ajmb.org)
We will apply our Treg model to thousands of DNA sequences (genomes) from patients with autoimmune disease to predict how genetic disease risk variants in this key immune cell type might drive disease. (cincinnatichildrens.org)
Microbiome research typically involves the study of all genomes present within a specific environment, such as soil, seawater or a human body site. (gbif.org)
For designing real-time detection assays, an efficient data structure and search algorithm are presented to identify the most distinguishing sequences of a pathogen that are absent from all other sequenced genomes. (umd.edu)
DNA methylation plays quite an important role in the mammalian genomes absolute functions. (slu.se)

We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. (springer.com)
MGnify is a free to use analysis platform and database of analysed microbiome sequencing projects, hosted by the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). (gbif.org)
The team also plans to characterize how these microbes respond at a molecular level to specific stress conditions, including altered gravity and atmospheric composition. (nasa.gov)
Manipulation of DNA is both an intrinsic and essential component of molecular biology and biotechnology. (dcu.ie)
Furthermore, the discovery of new molecular mechanisms by which small molecules modify DNA structure, reactivity, and biological repair contributes significantly to potential drug development. (dcu.ie)
In addition to the application of developmental metallodrugs as inducers of chemical nuclease activity, the effects of cytotoxic trinuclear platinum(II) complexes as high-affinity DNA binders that inhibit-or block-endonuclease enzyme recognition and excision are reported through a wide variety of biophysical and molecular biological methods. (dcu.ie)
The ribosomal operons mainly 16S rDNA has proven to be a stable and specific molecular marker for bacterial identification. (ispub.com)
These ribosomal sequences was functional for the phylogenetic analysis and molecular taxonomic of any bacteria. (ispub.com)
We are interested in understanding at the molecular level how recombination occurs and what roles are played by the many proteins involved in DNA recombination, repair and replication. (brandeis.edu)
Using synchronized cells undergoing recombination that is initiated at a specific site on a chromosome by an inducible endonuclease, we use physical monitoring techniques (Southern blots, PCR analysis) to follow the sequence of molecular events that occur in real time. (brandeis.edu)
These data have been combined with previously published LNET data to perform integrative analysis using multi-omics factor analysis (MOFA), resulting in a molecular map of lung neuroendocrine neoplasms for exploration. (who.int)
Multi-omics integration analysis of 319 carcinoids resulted in a molecular map forming a distinctive tetrahedron. (who.int)

rRNA sequence comparison of the ITS region confirmed N. sphaerica identity. (wikipedia.org)
In this study, we investigated fecal 16S rRNA gene sequencing analysis of changes in the gut microbiota of rats with LDA-related intestinal injury. (hindawi.com)
The fecal samples were then analyzed using high-throughput sequencing of 16S rRNA V3-V4 amplicons. (hindawi.com)
DNA from the isolates was extracted and the 16S rRNA gene was amplified using primers specific for Actinomycetes. (scirp.org)

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. (nature.com)
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. (nature.com)
Transcriptome analysis by strand-specific sequencing of complementary DNA. (mpg.de)
Characterizing the mouse ES cell transcriptome with Illumina sequencing. (mpg.de)
Purpose: GG-H whole transcriptome array analysis suggested involvement of PININ (PNN) in the alternative splicing of multiple long non-coding RNAs (lncRNAs). (molvis.org)

Euchromatin is a lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in genes, and is often (but not always) under active transcription. (bcgsc.ca)
For the vast majority of genes, the sequence in these regions was indeed finished. (bcgsc.ca)
Epigenetic analysis revealed a specific N 6 -methyl adenine (m 6 A) methylating pattern including methylation of alginate, flagellar and quorum sensing associated genes. (frontiersin.org)
Any change in the functional sequence of these genes could potentially be fatal. (slu.se)
This effort would use increasingly affordable sequencing technology to measure a defined set of genes that meet the evidentiary bars of high disease risk and effective intervention. (cdc.gov)
Regions of the L. killicki ( L. tropica ) and L. major genes sequences were scanned using BLAST program and subsequently compared using appropriate bioinformatic tools Chromas and MEGA. (who.int)
Researchers are working to determine how the loss of specific genes in this region contributes to the various features of the disorder. (medlineplus.gov)
These signs and symptoms are likely caused by the loss of specific genes in the deleted region. (medlineplus.gov)

These validated assemblies provide the ultimate nucleic acid diagnostic, revealing the entire sequence of a genome. (umd.edu)
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
The second approach, which attempted to detect AIDS virus-related nucleic acid sequences using dot blot hybridization analysis of the vaccine with an AIDS virus deoxyribonucleic acid (DNA) probe, was done at MSD using as a positive control infected cellular (ribonucleic acid) RNA preparations provided by CDC. (cdc.gov)

However, traditional Sanger sequencing-based DNA barcoding protocols can be prohibitively expensive and laborious when large community samples have to be processed. (springer.com)
Whole-exome data of the COL4A5 gene of the patient's family were analyzed using Sanger sequencing and online software was used to predict the conservation and pathogenicity of mutant amino acids within species evolution. (researchsquare.com)
Additionally, DNA Sanger sequencing was performed for genetic analysis. (bvsalud.org)

Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. (nature.com)
Massively parallel sequencing (MPS) data provides an opportunity to better characterize stutter, permitting a more accurate means of detecting both size- or longest uninterrupted stretch (LUS)-based stutter but also allele and motif-specific stutter characteristics. (ojp.gov)
Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. (mpg.de)

Although isolates of Phylogenetic analysis on the TPI sequences confirmed the G. duodenalis from humans and various animals are mor- formation of distinct groups. (cdc.gov)
Of the 120 strains of Variola virus in the Russian collection, 55 isolates had been selected for further investigation, involving viability studies, biological characterization and genome analysis. (who.int)
DNA had been isolated from the non-viable isolates. (who.int)
Analysis of the 451 isolates in the American collection revealed that some of these are Monkeypox virus , Camelpox virus or chimeric viruses prepared by recombination of variola viruses with other orthopoxviruses. (who.int)
In the present study, 26 A. simplex -like larval isolates were obtained from two Pacific cod landed in Hokkaido, Japan, and examined genetically by PCR-RFLP and direct sequencing of the ITS region of rDNA. (cambridge.org)
A multiplex polymerase chain reaction (PCR) assay was also developed as an alternative for identification of isolates, and was shown to be a rapid, sensitive and specific diagnostic assay. (who.int)

Most of the disease-associated genetic variants fall outside protein-coding sequences and overlap with "enhancers," regions of chromatin that control gene expression. (cincinnatichildrens.org)
The sequence analyses and quantification of splice variants of candidate lncRNAs, including RP11-295B20.2, RP11-18I14.1, and RP11-322M19.1, demonstrated complex configuration of their splicing changes, with a significant impact of PNN on the process. (molvis.org)
Knockdown of PNN in HCET cells led to specific changes in the inclusion of multiple cassette exons as well as in the use of alternative splice sites in RP11-322M19.1 and RP11-18I14.1, resulting in considerable net changes in the ratio between the splice variants. (molvis.org)
In principle, DNA-based population screening can identify persons with rare pathogenic variants who are at high risk of preventable diseases and disabilities and could benefit from early interventions. (cdc.gov)
Using the rationale of newborn screening for rare disorders for which a specific combination of features pertain (serious outcome, effective prevention of diseases and disabilities, asymptomatic latent period, and an affordable assay), James Evans and coauthors proposed in 2013 that DNA-based population screening for rare pathogenic variants could be an early low hanging fruit for the emerging field of public health genomics. (cdc.gov)
However, such an approach would miss carriers of rare pathogenic variants that are measured using sequencing technologies. (cdc.gov)
However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)

This study sheds light on the value of characterizing motif- and allele-specific stutter, including non-LUS stutter, when using MPS methods. (ojp.gov)
Motif- and allele-specific stutter models provide the most comprehensive analysis of sequence stutter rates and provide the ability to differentiate stutter sequences more accurately from true allele stutter. (ojp.gov)
OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. (umassmed.edu)

Underpinned by dramatically falling DNA sequencing costs, metagenomic analyses have become increasingly mainstream. (gbif.org)
We tested various specimens (blood, cerebrospinal fluid, intraocular fluid, serum, and tissues) from the organ donor and recipients by serology, RT-PCR, immunohistochemistry, metagenomic next-generation sequencing, and host gene expression, and conducted a traceback of blood transfusions received by the organ donor. (cdc.gov)
FINDINGS: We identified one read from yellow fever virus in cerebrospinal fluid from the recipient of a kidney using metagenomic next-generation sequencing. (cdc.gov)
INTERPRETATION: This investigation substantiates the use of metagenomic next-generation sequencing for the broad-based detection of rare or unexpected pathogens. (cdc.gov)

You've probably already heard - and have been hearing for the last 15 years - that the human genome has been sequenced. (bcgsc.ca)
For modeling and analysis - such as in cancer research, for example, which is what we do here - by far the most important parts of the human genome assembly are the parts that code for protein ( transcribed regions and their ORFs ), along with their adjacent regulatory sequences . (bcgsc.ca)
It and BGI, OpGen said, had already used the technology to complete a study based on human genome data to successfully close gaps in existing sequence folds. (genomeweb.com)
Rapid advances in human genome sequencing technologies have accelerated the integration of genomics into clinical practice. (cdc.gov)

Compared to LC-MS/MS, sequencing-based methods identify modified bases affiliated with their sequence context, which facilitates a comprehensive genome-wide analysis along with downstream functional studies 28 . (nature.com)
ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. (umassmed.edu)
Previous studies of DNA methylation suggest epigenetic alterations may also be important, but an integrated genome-wide analysis of genetic and epigenetic alterations in ALL has not been performed. (lu.se)

Exome sequencing from nanogram amounts of starting DNA: comparing three approaches. (mpg.de)
1 - DNA methylation quantification analysis in different human soft tussues for forensic purposes 2 - Whole exome sequencing data analysis for geneic alteration in heart malfunctioning. (slu.se)
We planned to conduct a study, based on the exome sequencing and analysis of DNA samples taken from the cases. (slu.se)

Alternatively spliced lncRNAs were detected with in situ hybridization with variant-specific RNA probes on human cornea sections. (molvis.org)
Finally, in situ hybridization analyses revealed the presence of RP11-295G20.2 in the nuclei of corneal epithelial cells, but not in the stromal cells of the human cornea, while RP11-322M19.1 was present in epithelial and non-epithelial cells. (molvis.org)

This package is for the visualization of multi-omics data that can be integrated into any analysis pipeline in R. trackViewer can be used not only to visualize coverage and annotation tracks, but also to generate lollipop and dandelion plots that depict sparse and dense methylation/mutation/variant data to facilitate an integrative analysis of diverse datasets. (umassmed.edu)
We find that there is a 1000-fold increase in mutation rate and that about half the mutations have a distinctive "signature" suggesting that the DNA polymerase frequently dissociates and re-anneals with its template. (brandeis.edu)
We performed pathogenicity analysis on the mutation and selected a suitable assisted reproductive technology solution for the patient. (researchsquare.com)
Biological information analysis revealed the mutation was pathogenic and preimplantation genetic diagnosis was adopted. (researchsquare.com)
Conclusion Genetic testing prior to pregnancy is recommended in Alport syndrome patients or family members prior to pregnancy to determine the specific location of the gene mutation. (researchsquare.com)
The reason for the observed defective assembly in E. coli is probably not some unidentified mutation in the plasmid DNA because the same plasmid preparation complemented a B. subtilis sdhCAB deletion strain [7]. (lu.se)

DNA sequencing is useful for determining the order of the precise nucleotides in a DNA molecule. (medgadget.com)
Approximately 74% of the nucleotides comprising coding sequences and splice junctions in the mouse genome were covered at least three times. (nih.gov)
Total 38 nucleotides and 36 proteins sequences of linA and linB were used for constructing the phylogeny. (ispub.com)

selected to develop GMM-specific detection methods that could be then directly applied on the food/feed matrices. (pulsus.com)
Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. (nature.com)
2. Develop additional strategies to deliver affordable, simple DNA based tools and protocols for the rapid, sensitive and specific Leishmania parasites detection concomitant to their identification/ differentiation. (who.int)

The crew set up hardware for Wet Lab-2 One-Step Gene Sampler Operations then performed mRNA expression analysis on a radish harvested from Plant Habitat. (nasa.gov)

scATACpipe enables users to perform the end-to-end analysis of scATAC-seq data with three sub-workflow options for preprocessing that leverage 10x Genomics Cell Ranger ATAC software, the ultra-fast Chromap procedures, and a set of custom scripts implementing current best practices for scATAC-seq data preprocessing. (umassmed.edu)
allow proceeding to the in silico comparative genomics analysis of Leishmania DNAs and annotating the sequences identified. (who.int)

1988. Species-specific response to the rodent carcinogens 1,2-dimethylhydrazine and 1,2-dibromo-3-chloropropane in rodent bone-marrow micronucleus assays. (cdc.gov)
Mediated Isothermal Amplification based assays for the selective and/or specific identification of, and discrimination among the two (2) Leishmania species encountered in Tunisia. (who.int)
The objective here is to develop LAMP assays specific for each of the Leishmania species so far encountered in Tunisia. (who.int)

However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)

Results are presented that show these "signature" sequences can be used to detect pathogens in complex samples and differentiate them from their non-pathogenic, phylogenetic near neighbors. (umd.edu)
11 And human diseases, including cancer in particular, tend to be defined by the presence of proteins with altered and pathogenic sequences. (biorxiv.org)

MGnify offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional/metabolic potential of environmental samples. (gbif.org)
Functional studies and RNA sequencing were performed after silencing the REG4 expression. (cancerindex.org)
METHODS: Functional analysis was conducted on the whole blood of seventeen male individuals who were suspected to have X-linked chronic granulomatous disease (CGD). (bvsalud.org)

We analyzed 137 B-lineage and 30 T-lineage childhood ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. (lu.se)

Earlier this month, the Gaithersburg, Md.-based firm announced a collaboration with BGI to evaluate the platform's utility for de novo sequence finishing in larger organisms. (genomeweb.com)

In the context of a process, the market has been segmented into data analysis, sample preparation, sequencing, and others. (medgadget.com)
The use of CE-based fragment data rather than sequence-based data, has limited the community's understanding of the precise behavior of stutter. (ojp.gov)
In the current study, analysis and characterization of stutter sequences was performed using data generated from 539 samples amplified with the ForenSeq and PowerSeq 46GY library preparation kit and sequenced on the Illumina MiSeq FGx. (ojp.gov)
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. (mpg.de)
Users of MGnify can submit their own data for analysis or freely browse all of the analysed public datasets held within the database. (gbif.org)
Data table showing topics related to specific cancers and associated disorders. (cancerindex.org)
One area that the company is focusing on is using the technology to arrive at high resolution analysis of an isolate and then using that data to compare the isolate with others that are associated with a public health outbreak. (genomeweb.com)
Using OpGen's MapSolver software, contigs generated by sequencers are mapped in silico "so that the contigs can be mapped back to the complete ordered optical map scaffold of DNA, giving researchers the ability to very rapidly orient the sequence data to help accelerate assembly and finishing," he said. (genomeweb.com)
Conclusions: The data suggest PNN's role in the alternative splicing of a specific subset of lncRNAs might have a significant impact on the corneal epithelium. (molvis.org)
Impact of fatty liver on long-term outcomes in chronic hepatitis B: a systematic review and matched analysis of individual patient data meta-analysis. (stanford.edu)
Via a systematic review, conventional meta-analysis (MA) and individual patient-level data MA (IPDMA), we compared liver-related outcomes and mortality between CHB-FL and CHB-no FL patients.We searched 4 databases from inception to December 2021 and pooled study-level estimates using a random-effects model for conventional MA. (stanford.edu)
scATACpipe is a bioinformatic pipeline (powered by Nextflow) for single-cell ATAC-seq (scATAC-seq) data analysis. (umassmed.edu)
NADfinder is the first software designed specifically for the bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation. (umassmed.edu)
2. Identify and apply appropriate techniques of data analysis. (aber.ac.uk)
Students will be expected to develop skills in preparing and inputting data, spreadsheets, word processing and research-specific analysis programs to analyse results appropriate to their project. (aber.ac.uk)
Methods A retrospective analysis of clinical and genetic data of a patient with Alport syndrome was performed. (researchsquare.com)
Epidemiologic approaches to detect an association between HB vaccine and AIDS have included analysis of data on AIDS cases reported to CDC concerning their receipt of HB vaccine and monitoring rates of AIDS in groups of homosexually active men who did or did not receive HB vaccine in the vaccine trials conducted by CDC in Denver, Colorado, and San Francisco, California. (cdc.gov)
Differential gene expression and patient prognosis analyses were performed using gene expression data obtained from public databases. (bvsalud.org)
The sequences were analyzed in silico by BLAST searching for homologies with other DNAs deposited in the local and public data bases. (who.int)
BASE was initially developed to manage array-based data but is now extended to support storage and analysis of sequencing data. (lu.se)
Analyses include generation of gene expression and sequencing data with the ultimate goal to build an infrastructure for future real-time clinical implementation. (lu.se)
Analysis and execution of standard analysis pipelines for sequencing data will be performed through BASE. (lu.se)
thirdly, an external file system for storage of sequencing data that are referenced from BASE. (lu.se)
This implies interplay with adopting the BASE software (the Reggie extension is an example of adaptation on BASE to specific needs in SCAN-B) and the laboratory work to achieve efficient data collection. (lu.se)

The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
In addition to RNA-associated silencing and histone modification, a major epigenetic mechanism in higher-order eukaryotes is DNA methylation. (qiagen.com)

In the last two decades, DNA barcoding, the sequencing of short species-specific amplicons, has considerably simplified community analyses (Hebert et al. (springer.com)

On the basis of 16S rDNA phylogenetic analysis of bacteria was done. (ispub.com)

In addition, an independent cohort of 55 clinical samples was analyzed by quantitative real-time PCR analysis. (cancerindex.org)
The results were validated both by gene expression analysis and immunohistochemistry study in an independent 55 clinical samples from Fudan University Shanghai Cancer Center. (cancerindex.org)
QIAseq Targeted Methyl Panels deliver high mapping efficiency (figure QIAseq Targeted Methyl Panel: mapping efficiency Input >1 ng – gDNA – FFPE – ccfDNA Results show high mapping on primer and high unique mapping. "> QIAseq Targeted Methyl Panel: mapping efficiency ), high reproducibility (figure QIAseq Targeted Methyl Panel: methylation degree reproducibility To test methylation degree accuracy and reproducibility, 40 ng control DNA with 0%, 50% and 100% methylation were processed using the QIAseq Targeted Methyl Panel, which consisted of 749 primers. Samples were sequenced on MiSeq and methylation degree of CpG covered by >30 UMI was evaluated, resulting in accurate and highly reproducible methylation calling. "> QIAseq Targeted Methyl Panel: methylation degree reproducibility ) and high correlation with established methods (figures QIAseq Targeted Methyl Panel - high correlation with established methods To test correlation with established methods, the QIAseq Targeted Methyl Panel was used with 40 ng input gDNA from hepatocytes. The panel consisted of 102 primers, covering 71 CpGs. Compared to the Supplier I array, methylation degree resulted in high correlation. "> QIAseq Targeted Methyl Panel - high correlation with established methods and QIAseq Targeted Methyl Panel: methylation status of FFPE DNA: methylation degree To test methylation status of FFPE DNA, the QIAseq Targeted Methyl Panel was used with 40 ng input FFPE DNA. The panel consisting of 93 primers covered 566 CpG sites. The evaluated methylation degree of 7 CpG sites of the MGMT gene highly correlates to the methylation degree that was previously validated with Pyrosequencing. "> QIAseq Targeted Methyl Panel: methylation status of FFPE DNA: methylation degree ). (qiagen.com)
It enables faster genetic analysis of multiple samples without the need to destroy the specimen, as traditional technology requires. (nasa.gov)

Differential gene expression analysis indicated that this isolate formed excessive biofilm by reducing flagellar formation (7.4 to 1,624.1 folds) and overproducing extracellular matrix components including CdrA (4.4 folds), alginate (5.2 to 29.1 folds) and Pel (4.8-5.5 folds). (frontiersin.org)
For strain typing, an optical map of the isolate of interest can be generated in about 24 hours, compared to the days or weeks that it would take with next-generation sequencing-based methods. (genomeweb.com)
In addition, OpGen's technology "gives you much more distinguishing features and gives you the ability to identify down to the strain in an isolate level," unlike pulsed field gel electrophoresis, which White said is the gold standard method for separating DNA molecules. (genomeweb.com)
The technology also provides enough granularity to determine whether there are specific motifs within the isolate that may be associated with virulence or antibiotic resistance, White said. (genomeweb.com)
Recently, metagenomics a new approach to identify culturable and non culturable bacteria with the help of 16S rDNA sequences isolate total DNA from HCH contaminated soil and amplified 16S rDNA through universal primers and confirmed its total population with denaturing gradient gel electrophoresis and sequencing. (ispub.com)

In a pedigree of C57BL/6J mice homozygous for germline mutations induced by the mutagen N-ethyl-N-nitrosourea (ENU), numerous animals died under specific pathogen-free (SPF) conditions between 6 and 7 months of age. (nih.gov)
Genetic mapping by bulk segregation analysis excluded all mutations but this one as the cause of renal disease in Aoba mice. (nih.gov)
As a result, mutations, such as insertions, inversions, and deletions that may be missed with sequencing technologies can be found with the Optical Mapping System, and, similarly, contig misassemblies can be identified and corrected. (genomeweb.com)
DNA sequencing of the CYBB gene identified specific mutations in each patient. (bvsalud.org)
Findings from experiments conducted so far suggest that the specific defects could be small inframe deletions, inframe additions, or point mutations. (medscape.com)

Traditionally, DNA profiles are obtained using capillary electrophoresis (CE), where amplified DNA fragments are separated by size, not sequence, and the identification of stutter is performed on a locus-specific level. (ojp.gov)
A total of 10 of these calls, all homozygous, were validated by capillary sequencing. (nih.gov)

There are multiple published methods for strand-specific RNA-seq, but no consensus exists as to how to choose between them. (nature.com)
Weighing each method's performance and ease, we identified the dUTP second-strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing. (nature.com)
Figure 1: Methods for strand-specific RNA-seq. (nature.com)
These methods are potentially the future of diagnostics, but each requires sophisticated computational design or analysis to operate effectively. (umd.edu)

DNA meth-ylation represses transcription by interfering with transcription factor binding and indirectly by recruiting methyl-CpG-binding proteins and reducing chromatin remodeling activities ( 12 ). (spandidos-publications.com)
We have shown that the invasion of DNA strands into a donor template region requires the action of the chromatin remodeling protein Rad54 that enables the recombination machinery to gain access to "closed" regions of DNA. (brandeis.edu)
The two donor loci are maintained in a chromatin configuration that prevents them from being transcribed or being cleaved by the HO endonuclease that cuts the same sequence at MAT to initiate switching. (brandeis.edu)

The amplified gene was sequenced and phylogeny analysis was done. (scirp.org)

Figure 6: Digital expression profiling using strand-specific RNA-seq. (nature.com)
Importantly, enhancers are typically context-specific, contributing to gene expression in particular cell types (e.g., skin, brain) under particular conditions (e.g., in response to nutrients or a pathogen). (cincinnatichildrens.org)
Moreover, DNA hypomethylation of the COX‑2 promoter region located from ‑1,522 to ‑829 bp might contribute to transcriptional regulation of COX‑2 expression and induce a pro‑inflammatory response in KIC. (spandidos-publications.com)
thus, Pnn may affect crucial alternative splicing (AS) decisions and, in turn, impact cell-type specific gene expression. (molvis.org)
Cloning and expression of the gene for lactacin F, a Lactobacillus acidophilus bacteriocin, using an amino acid sequence-derived DNA probe. (ncsu.edu)
CLONING, EXPRESSION, AND NUCLEOTIDE-SEQUENCE OF THE LACTOBACILLUS-HELVETICUS-481 GENE ENCODING THE BACTERIOCIN HELVETICIN-J. JOURNAL OF BACTERIOLOGY, 172(11), 6339–6347. (ncsu.edu)
We found that the different genetic subtypes of ALL are characterized by distinct DNA methylation signatures that exhibit significant correlation with gene expression profiles. (lu.se)
The first example describes a research project involving sequencing based gene expression analysis and the second example describes a microarray service facility use of BASE. (lu.se)

G. microti and nucleotide sequence characterization of The taxonomy of Giardia at the species level is compli- amplified TPI fragment. (cdc.gov)
This information provides a foundation for including the characterization of non-LUS stutter products when analyzing DNA profiles, specifically mixtures with potential low-level contributors. (ojp.gov)

We opted for conserved sequences between species, presenting enough sequence heterogeneities to be considered for the design of species- specific LAMP primers: such primers would allow the selective amplification of the DNA targets. (who.int)
The sequences identified in the previous section of the work were used to design a combinations of 6 primers in 8 distinct regions of the target sequences for the amplification of a selection of reference DNAs belonging to the different Old World Leishmania species. (who.int)

In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. (springer.com)

According to a procedure that has been previously validated for the identification of species - specific targets among which some fragments would fit into the second category of sequences expected. (who.int)

The overall aim within the group is to predict recurrences by monitoring breast cancer specific proteins in tumors and patient blood, primarily using a combination of the DNA sequence and mass spectrometric analysis and to translate these findings into clinical routine work. (lu.se)

In contrast, the Ten-Eleven-Translocation (TET) dioxygenase family, including TET1, TET2 and TET3, mediates active DNA demethylation and hydroxylate-methylated DNA by converting 5-methylcyto-sine to 5-hydroxymethylcytosine to regulate DNA methylation status. (spandidos-publications.com)

All pure DNA templates from S. epidermidis generated a detectable amplicon by 264 bp length, but the PCR test was negative for the non- S. epidermidis group. (ajmb.org)
Results show that although the LUS sequence stutters at a higher rate than non-LUS motifs, the non-LUS stutter products do occur at detectable levels and potentially influence sequence-based mixture analysis. (ojp.gov)
The vaccine contained no detectable AIDS virus-related sequences at a sensitivity of less than one picogram of DNA per 20-ug dose of vaccine. (cdc.gov)

High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. (springer.com)
We have shown that this regulation involves the action of a small Recombination Enhancer (RE) sequence that enables a donor on the left chromosome arm to recombine preferentially in MATa cells. (brandeis.edu)

To cite MGnify, please refer to the following publication: EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. (gbif.org)
RT-PCR products from six patients who died from TBE between 2013 and 2017 were directly sequenced and analysed phylogenetically. (who.int)

We are interested in determining what are the specific biochemical roles played by the many proteins implicated in DNA recombination, repair and replication. (brandeis.edu)
We have identified the proteins necessary to carry out the initial steps in strand invasion and the beginning of new DNA synthesis, which is significantly different from the normal process of replication. (brandeis.edu)
This is the process we have studied most intensively, but we are also interested in an alternative process known as break-induced replication (BIR), where only one end of a chromosome break locates a template sequence and assembles a complete replication fork and can copy sequences to the end of a chromosome, producing a nonreciprocal translocation. (brandeis.edu)

We used bisulphite (pyro) sequencing to quantify the DNA methylation and confirmed that the regions are different with respect to their DNA methylation content. (slu.se)

We hope that these approaches will uncover breast cancer specific changes that will define new biomarkers distinguishing patients with an increased risk of developing LR. (lu.se)

The disease characteristics of AS mainly include progressive glomerulonephritis, renal failure, sensorineural deafness, and specific ocular abnormalities (lenticular nucleus and macular spots). (researchsquare.com)

DNA sequence and analysis of human chromosome 9. (nih.gov)
Chromosome 18 spans about 78 million DNA building blocks (base pairs) and represents approximately 2.5 percent of the total DNA in cells. (medlineplus.gov)

Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional. (nih.gov)

For example, most human tissues in healthy individuals acquire somatic nucleotide substitutions, insertions, deletions and DNA rearrangements, leading to the production of variant protein isoforms. (biorxiv.org)

We will build mathematical models to predict how a patient's DNA sequence changes gene regulation (by enhancers) in particular cell types. (cincinnatichildrens.org)

Together, these results demonstrate subtype- and disease-specific alterations in cytosine methylation in ALL that influence transcriptional activity, and are likely to exert a key role in leukemogenesis. (lu.se)

Figure 2: Key criteria for evaluation of strand-specific RNA-seq libraries. (nature.com)
A strand-specific library preparation protocol for RNA sequencing. (mpg.de)

Market Research Future (MRFR) recently launched a report on DNA Sequencing Market Research Report - Forecast to 2023, that declares this market could see an expansion at 17.64 % CAGR between 2018 and 2023. (medgadget.com)

Anatomy13

Organisms21

Diseases2

Chemicals and Drugs74

Analytical, Diagnostic and Therapeutic Techniques and Equipment42

Phenomena and Processes108

Disciplines and Occupations3

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science6

Health Care7

Geographicals2

Genomic23

Whole-genome10

Genomes6

Molecular12

RRNA4

Transcriptome5

Genes8

Nucleic3

Sanger3

Massively parallel3

Isolates6

Variants7

Allele3

Metagenomic4

Human genome4

Genome-wide analysis3

Exome3

Hybridization2

Mutation6

Nucleotides3

Detection3

MRNA1

Genomics2

Assays3

Proteins sequences1

Pathogenic2

Functional3

Microarray analysis1

Novo1

Data24

Epigenetic2

Amplicons1

Phylogenetic analysis1

Samples4

Isolate5

Mutations5

Capillary2

Methods4

Chromatin3

Phylogeny1

Expression8

Characterization2

Primers2

Advances1

Species-specific1

Clinical1

Methylation status1

Detectable3

Enables2

20172

Replication3

Quantify1

Biomarkers1

Renal1

Chromosome2

Genetics1

Tissues1

Patient's1

Transcriptional1

Strand-specific2

20181