Organisms genomic library. Medical search. Frequent questions

They have played an important role in the whole genome sequencing of several organisms, including the human genome and several model organisms. (wikipedia.org)
These are due to the advance of genome-wide association studies from the ability to create and sequence genomic libraries. (wikipedia.org)
Below are the steps for creating a genomic library from a large genome. (wikipedia.org)
This combination maximizes the conversion rate of sample DNA into the NGS library, while efficiently and evenly amplifying even high and low GC content regions of the genome. (qiagen.com)
The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (usda.gov)
Since the genome of an organism is fixed, chromosomal DNA may be isolated from almost any cell type in order to prepare genomic DNA. (biologydiscussion.com)
By digesting complex genomic DNA from an organism it is possible to reproducibly divide its genome into a large number of small fragments, each approximately the size of a single gene. (biologydiscussion.com)
We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. (nih.gov)
Illumina sequencing enables a wide variety of applications, allowing researchers to ask virtually any question related to the genome, transcriptome, or epigenome of any organism. (manchester.ac.uk)
Furthermore, molecular cloning serves as the foundation for constructing genomic libraries, which are comprehensive collections of cloned DNA fragments representing an organism's entire genome. (axis-shield-density-gradient-media.com)
To see full example code for de novo machine learning, prediction of sgRNA activity for desired loci, and construction of new genome-scale CRISPRi/a libraries, see the CRISPRiaDesign_example_notebook (included as Jupyter notebook or web page ). (github.com)
Links are to human genome files relied upon for the hCRISPRi-v2 and hCRISPRa-v2 machine learning--and required for the Library_design_walkthrough--but any organism/assembly may be used for design of new libraries or de novo machine learning. (github.com)
The objective of this study was to apply optimized methods to purify C. cayetanensis oocysts and extract DNA in order to obtain high-quality whole genome sequences with minimum contamination of DNA from other organisms. (cdc.gov)
MiSeq sequencing reads were taxonomically profiled for contamination, de novo assembled, and mapped to a draft genome available in GenBank to assess the quality of the resulting genomic sequences. (cdc.gov)
Conclusions: Density gradients performed in the presence of a detergent followed by flow cytometry sorting of oocysts yielded sufficient genomic DNA largely free from contamination and suitable for whole genome sequencing of C. cayetanensis. (cdc.gov)
Libraries were sequenced on the Genome Analyzer II or IIx following the manufacturer's protocols. (nih.gov)
Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. (lu.se)
The systematic study of the complete DNA sequences (GENOME) of organisms. (bvsalud.org)
Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES. (bvsalud.org)

These nucleic acid polymers encode for the all of the materials an organism needs to live in the form of genes. (wikibooks.org)
As a result of ocean exploration and research, genomic libraries can be created to preserve all of the genes (DNA) found in marine organisms. (noaa.gov)
A DNA library is a set of cloned fragments that collectively represent the genes of a particular organism. (biologydiscussion.com)
Particular genes can be isolated from DNA libraries, much as books can be obtained from conventional libraries. (biologydiscussion.com)
These libraries provide researchers with a valuable resource for studying genes, their regulatory elements, and their functions. (axis-shield-density-gradient-media.com)
Note that all sgRNA designs for CRISPRi/a human/mouse protein-coding gene libraries are included as supplementary tables in the eLife paper, so cloning of individual sgRNAs or construction of any custom sublibraries targeting protein-coding genes can simply refer to those tables. (github.com)
These scripts are primarily useful for the design of sgRNAs targeting novel or non-coding genes, or for organisms beyond human and mouse. (github.com)
The term "transcriptome" refers to the set of genes that are expressed or transcribed from genomic DNA in a particular cell or tissue. (the-scientist.com)
Shotgun metagenomics allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. (igatechnology.com)
However, when applying this concept to genomes of multicellular organisms such as mammals, one has to deal with a large number of false positive predictions since many transcription factor genes are only expressed in specific tissues or cell types. (lu.se)
We developed TS-REX, a database/software system that supports the analysis of tissue and cell type-specific transcription factor-gene networks based on expressed sequence tag abundance of transcription factor-encoding genes in UniGene EST libraries. (lu.se)

Generally, libraries made from organisms with larger genomes require vectors featuring larger inserts, thereby fewer vector molecules are needed to make the library. (wikipedia.org)
For organisms with very small genomes (~10 kb), the digested fragments can be separated by gel electrophoresis. (wikipedia.org)
The genomes of cellular organisms are composed of DNA. (proprofs.com)
Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. (fsu.edu)
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)
Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)

The vector containing the inserted fragments of genomic DNA can then be introduced into a host organism. (wikipedia.org)
The recombinant DNA is then introduced into a host organism. (pressbooks.pub)
The resulting recombinant DNA is then introduced into a host organism, such as bacteria or yeast, where it can be replicated and propagated. (axis-shield-density-gradient-media.com)

When experiment-specific spectrum library generation is either impossible or impractical, as is frequently the case with non-model organisms, sequence variants, splice isoforms, or scarce sample quantities, software tools such as Pecan 10 and DIA-Umpire 11 can detect peptides from DIA experiments without a spectrum library by directly searching every peptide in FASTA databases. (nature.com)
Over time, a succession of new genomic technologies has enabled investigators to interrogate single-base sequence analyses in clinically informative settings. (plos.org)
In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. (usda.gov)
Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. (usda.gov)
This means that digesting genomic DNA with EcoRI, which recognizes the sequence 5′-GAATTC-3′, will produce fragments each of which is, on average, just over 4 kb. (biologydiscussion.com)
The term "cloning" refers to the replication of a specific DNA sequence or an entire organism, and in the molecular biology context, it primarily involves the generation of identical copies of a DNA fragment. (axis-shield-density-gradient-media.com)
Next-Generation Sequencing, with its ability to sequence thousands of organisms in parallel, has revolutionized microbiology by allowing concurrent analysis of whole microbial communities from complex samples and identification of strains that may not be found using other methods. (igatechnology.com)
Since the collection of DNA from an environment is largely uncontrolled, it is important to remember that the most abundant organisms in an environmental sample are most highly represented in the resulting sequence data. (igatechnology.com)
However, the random nature of shotgun sequencing ensures that many of these organisms, which would otherwise go unnoticed using traditional culturing techniques, will be represented by at least some small sequence segments. (igatechnology.com)

One of the main workshop goals was to alleviate this problem by enhancing a reference library of genetic sequences from positively identified marine benthic organisms. (gulfresearchinitiative.org)
This study examined potential gene sequences identified in EST libraries of soybean and assigned the potential gene sequences with molecular functions. (usda.gov)
Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (usda.gov)
Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (usda.gov)
By using next generation sequencing, genomic sequences can be obtained and compared to identify potential genotyping markers. (cdc.gov)
The methods described here will facilitate the accumulation of genomic sequences from various samples, which is a prerequisite for the development of typing tools to aid in outbreak investigations. (cdc.gov)
Primers are tailed with sequences to incorporate indexing barcodes, and samples are pooled into a single library for sequencing on Illumina MiSeq sequencing system . (igatechnology.com)
In contrast, complementary DNA (cDNA) libraries contain only those DNA sequences that are complementary to messenger RNA (mRNA) molecules present in a cell and differ from one cell type to another. (pharmacy180.com)
After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size selected from a 8% polyacrylamide gel. (nih.gov)
The prediction of transcription factor binding sites in genomic sequences is in principle very useful to identify upstream regulatory factors. (lu.se)

Standard library preparation methods that apply to many sample types - such as circulating cell-free DNA, FFPE DNA, ancient DNA and ChIP-seq DNA - can result in quality-related problems. (qiagen.com)

The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. (re3data.org)
Prokaryotic organisms normally contain small, circular, extrachromosomal DNA molecules called plasmids that can serve as vectors. (pharmacy180.com)

A similar method can be used to titer genomic libraries made with non-viral vectors, such as plasmids and BACs. (wikipedia.org)
Isolation of clonable DNA (genomic libraries, cDNA synthesis) cloning vectors (plasmids, bacteriophages, cosmids) plasmid incompatibility and control of copy number. (up.ac.za)
Name an eukaryotic organism that has plasmids, and can be used as a host in gene cloning experiments. (mcqexams.com)

A genomic library is a collection of overlapping DNA fragments that together make up the total genomic DNA of a single organism. (wikipedia.org)
In order to construct a genomic library, the organism's DNA is extracted from cells and then digested with a restriction enzyme to cut the DNA into fragments of a specific size. (wikipedia.org)
It is important to note that every copy of a given DNA molecule from a specific organism will give the same set of fragments when digested with a particular enzyme. (biologydiscussion.com)
DNA from different organisms will, in general, give different sets of fragments when treated with the same enzyme. (biologydiscussion.com)
Nuclei were then treated with 45u of DNase I for 3 minutes at 25°C. Resulting genomic DNA was size fractionated and small (double cut) fragments were sequenced using Illumina technology. (nih.gov)
A DNA library is a collection of cloned restriction fragments of the DNA of an organism. (pharmacy180.com)
A genomic library is a collection of fragments of dsDNA obtained by digestion of the total DNA of the organism with a restriction endonuclease and subsequent ligation to an appropriate vector. (pharmacy180.com)

PCR may also establish the unique identity of a marine organism. (noaa.gov)
A formidable challenge was presented by the high degree of heterozygosity between the two haplotypes of the selected male representative of this marine organism. (nih.gov)

Datanator is composed of an integrated database of genomic and biochemical data, a web application for identifying relevant data for modeling a specific organism in a specific environmental condition, this REST API, and a Python library for programmatically discovering data for large models such as whole-cell models. (biocatalogue.org)

Construction of a genomic library involves creating many recombinant DNA molecules. (wikipedia.org)
These recombinant molecules are taken up by a host bacterium by transformation, creating a DNA library. (wikipedia.org)
Direct and indirect methods for the identification of recombinant organisms. (up.ac.za)
Recombinant DNA technology is the artificial recombination of DNA from two organisms. (pressbooks.pub)

Primarily using the technology and equipment of 10X Genomics , these approaches are providing insights into the cell types found in healthy and diseased tissues in humans and during development of model organisms. (manchester.ac.uk)
A large amount of data is being generated in the post genomic era through research in genomics, proteomics, and structural biology. (lu.se)

These consistent conversion rates of genomic information to adapter-ligated library molecules cover a 1000-fold range - from 10 pg to 10 ng of DNA input - and set an industry-leading benchmark. (qiagen.com)
These problems limit the utility of the data generated, from low library yield or conversion rates to high percentages of reads derived from adapter dimer molecules. (qiagen.com)

Telomere resolution and genomic instability in mouse. (ubc.ca)
The damage theories proposed the nine hallmarks that were generally considered to contribute to the aging process: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. (medchemexpress.com)

The main consideration in the construction of genomic or cDNA libraries is, therefore, the nucleic acid starting material. (biologydiscussion.com)

2016. Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions. (nih.gov)
RNA-seq 100-200mg of tissue was ground in liquid nitrogen and total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma), RNA was treated with DNase I and Ribo-Zero Plant leaf kit (Epicentre) and libraries were prepared using the TruSeq kit v2 (Illumina). (nih.gov)
Genomic DNA was used to construct Ovation Ultralow libraries for Illumina sequencing. (cdc.gov)

Search genomic information by chromosomal position. (wilmington.edu)

Our method specifically enables rapid, experiment-specific library generation for non-model organisms, which we demonstrate using the malaria parasite Plasmodium falciparum , and non-canonical databases, which we show by detecting missense variants in HeLa. (nature.com)

An organism's genomic DNA is extracted and then digested with a restriction enzyme. (wikipedia.org)

These results illustrated the possibility of studying the mechanism of VHb action in E. coli as a surrogate host, and were also indicative of the potential applicability of such a genetic strategy in organisms other than Vitreoscilla. (caltech.edu)
The NIEHS Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET) Program seeks to understand how environmental exposures lead to epigenetic changes-that is, modifications to DNA that affect gene expression without altering the underlying genetic code. (medlineplus.gov)

Next, the vector DNA can be taken up by a host organism - commonly a population of Escherichia coli or yeast - with each cell containing only one vector molecule. (wikipedia.org)

Calculating the titer allows researchers to approximate how many infectious viral particles were successfully created in the library. (wikipedia.org)
This allows researchers to also determine the percentage of infectious viral particles actually carrying a fragment of the library. (wikipedia.org)
By doing this test, researchers can also determine the efficiency of the ligation and make adjustments as needed to ensure they get the desired number of clones for the library. (wikipedia.org)

These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms. (harvard.edu)
The QIAseq Ultralow Input Library Kit is intended for molecular biology applications. (qiagen.com)
Suppliers of Whole-organism cDNA Libraries Suppliers of Tissue-specific cDNA Libraries The questions of gene function, interaction, and regulation are central to the science of molecular biology. (the-scientist.com)
Watson Library has a variety of books and eBooks on Biology and related topics. (wilmington.edu)
From mass extinction to immunity, and from sociobiology to swarm behaviour, 50 Biology Ideas You Really Need to Know will open you eyes to the fundamental biological processes that are essential to all life on earth, beginning with innovations unique to animals - such as the development of muscles and importance of circulation - and moving through to genetics, cells, tissues and, finally, the nature of groups of organisms. (wilmington.edu)

Polymerase chain reaction (PCR) is an important technique for establishing the presence of a particular gene in an organism. (noaa.gov)
Name the source organism that possesses Taq polymerase. (mcqexams.com)

The Genomic Technologies Core Facility incorporates bioinformatics analyses to facilitate a complete service from experimental design through to data analyses. (manchester.ac.uk)

For example, in the search for new antitumor compounds, primers from a conserved class of antitumor compounds can be used to find the presence of this type of gene in new organisms. (noaa.gov)

Read this article to learn about the gene libraries, genomic libraries and cDNA libraries. (biologydiscussion.com)
However, if the goal is the production of new or modified proteins, or the determination of tissue-specific expression of timing patterns, cDNA libraries are more appropriate. (biologydiscussion.com)
In contrast, however, cDNA libraries represent only mRNA being produced from a specific cell type at a particular time in the cell's development. (biologydiscussion.com)
Thus, it is important to consider carefully the cell or tissue type from which the mRNA is to be deriver in the construction of cDNA libraries. (biologydiscussion.com)
The sheer number of companies offering premade and custom cDNA libraries and products that facilitate their use serves as evidence of the tool's sustained power and efficacy. (the-scientist.com)

The applications of molecular cloning are diverse, ranging from gene manipulation and expression to the creation of genetically modified organisms (GMOs) with desired traits. (axis-shield-density-gradient-media.com)

We demonstrate a library generation workflow that leverages fragmentation and retention time prediction to build libraries containing every peptide in a proteome, and then refines those libraries with empirical data. (nature.com)
Our long-term goal is to make prediction about how organisms will adapt to living in a contaminated future world in both water and land environments. (lu.se)

Using a host cell to carry the vector allows for easy amplification and retrieval of specific clones from the library for analysis. (wikipedia.org)
After a genomic library is constructed with a viral vector, such as lambda phage, the titer of the library can be determined. (wikipedia.org)
The choice of vector also depends on whether a genomic library or cDNA library is constructed. (biologydiscussion.com)
a) Name any one organism used as vector. (mcqexams.com)

If the ultimate aim understands the control of protein production for a particular gene or its architecture, then genomic libraries must be used. (biologydiscussion.com)

These new research tools will answer questions about ecology, biodiversity, evolutionary genetics and systematics of marine organisms. (noaa.gov)
Addresses biodiversity, the characteristics organisms, and evolutionary history. (wilmington.edu)

Proper segregation of replicated chromosomes is essential for cell division in all organisms. (ubc.ca)
Chromosomes, Artificial, Yeast" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)

Most importantly, these libraries are built at the expense of time, sample, and considerable effort with offline fractionation, especially considering that they are typically not reusable across laboratories or instrument platforms 9 . (nature.com)
While this method is often prohibitively expensive because it requires enough instrument time and protein content for multiple injections for each sample, the use of multiple GPF injections can be applied just to pooled samples to generate DIA-only chromatogram libraries that make it easier to detect peptides in single-injection DIA experiments 13 . (nature.com)
However, even when using GPF, these tools still generally detect fewer peptides than library search engines, which can leverage previously acquired instrument-specific fragmentation and measured retention times. (nature.com)

The low percentage of adapter dimers minimizes library contamination compared to the competition. (qiagen.com)
This protocol enables the highest possible yield sequencing library, free of adapter dimer contamination - starting from a little as 10−100 pg* of DNA input. (qiagen.com)

The main objective of research in my laboratory is to understand how environmental pollutants interfere with and change biological processes in organisms from natural, wild populations. (lu.se)

The QIAseq Ultralow Input Library Kit incorporates new, ultra-efficient end-repair and ligation chemistries into a complete and streamlined solution. (qiagen.com)
QIAseq Ultralow Input Library Kits start with double-stranded DNA that has been fragmented enzymatically, chemically, mechanically or naturally. (qiagen.com)

The workshops were part of the Gulf of Mexico Research Initiative (GoMRI) research funded project " Genomic Responses to the Deepwater Horizon Event and Development of High- Throughput Biological Assays for Oil Spills ," The National Science Foundation also provided support for this effort. (gulfresearchinitiative.org)

To do this, dilutions of the library are used to transform cultures of E. coli of known concentrations. (wikipedia.org)
A test ligation of the library can be used to transform E. coli. (wikipedia.org)

These kits allow the generation of high-quality libraries from limited and damaged DNA sample types using an efficient, 2.5-hour workflow - starting from 10 pg-100 ng fragmented DNA for a robust library preparation suitable for a wide range of research applications. (qiagen.com)
Our workflow begins with purified genomic DNA. (igatechnology.com)

The choice of the particular type of gene library depends on a number of factors, the most important being the final application of any DNA fragment derived from the library. (biologydiscussion.com)

However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. (lu.se)

After genomic DNA has been isolated and purified, it is digested with restriction endonucleases. (biologydiscussion.com)

Data-independent acquisition approaches typically rely on experiment-specific spectrum libraries, requiring offline fractionation and tens to hundreds of injections. (nature.com)
Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. (fsu.edu)
While NGS technology is continuously improving, library preparation remains a process bottleneck for many labs and a limiting factor in the types of samples that can successfully generate NGS data. (qiagen.com)
The genomic data from these species will be crucial additions to the metagenomics reference library because most of the species had never been sequenced before. (gulfresearchinitiative.org)
Comprehensive next-generation sequencing (NGS) solutions including library preparation, sequencing systems, and data analysis. (manchester.ac.uk)
For convenience, the files referenced in Library_design_walkthrough in the folder "large_data_files" are also available here . (github.com)
Biofilm samples from shallow and deep periodontal sites will be evaluated for levels of recognized periodontal pathogens and selected organisms based on diversity data by RNA-oligonucleotide quantification technique (ROQT). (fapesp.br)

The method provides information both about which organisms are present and what metabolic processes are possible in the community . (igatechnology.com)

and a cDNA library, which represents the mRNA from a cell or tissue at a specific point of time. (biologydiscussion.com)

Model authors can freely publish their model source code in the Computational Model Library alongside narrative documentation, open science metadata, and other emerging norms that facilitate software citation, archival, interoperability, and reuse. (comses.net)

If the DNA that is introduced comes from a different species, the host organism is now considered to be transgenic. (pressbooks.pub)

Participants identified specimens to the lowest taxonomic level possible and then transferred them into vials for subsequent genomic sequencing at the Smithsonian National Museum of Natural History. (gulfresearchinitiative.org)

The molecular biologist begins his or her research when samples of marine organisms reach the surface. (noaa.gov)
These developed HT-NGS strategies addressed our anticipated future needs of throughput sequncing and cost, in a way which enabled its potential multitude of current and future applications in mammalian genomic research. (springer.com)
The HT-NGS is one of the great challenges of today's genomic research. (springer.com)
This platform accelerates research, requiring just 15 minutes total hands-on time and no amplification, cDNA conversion, or library prep, generating publication ready figures in roughly 24 hours. (manchester.ac.uk)
This library is a useful tool for anti-aging research. (medchemexpress.com)

Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches. (lu.se)

The taxonomists provided comprehensive overviews and elaborated on the morphology, current taxonomic status and systematic classification, ecology, and natural history of the different organism groups. (gulfresearchinitiative.org)

Anatomy7

Organisms33

Diseases3

Chemicals and Drugs57

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes109

Disciplines and Occupations2

Anthropology, Education, Sociology and Social Phenomena2

Technology, Industry, Agriculture5

Information Science28

Named Groups1

Health Care6

Genome19

Genes11

Genomes6

Introduced into a host organism3

Sequence9

Sequences10

ChIP-Seq1

Prokaryotic2

Plasmids3

Fragments7

Marine organism2

Specific organism1

Recombinant4

Genomics2

Molecules2

Telomere2

Nucleic acid1

Illumina3

Chromosomal1

Model organisms1

Organism's1

Genetic2

Molecule1

Researchers3

Biology5

Polymerase2

Analyses1

Primers1

CDNA libraries5

Genetically1

Prediction2

Vector4

Particular gene1

Evolutionary2

Chromosomes2

Instrument3

Contamination2

Populations1

Ultralow2

Responses1

Coli2

Workflow2

Type of gene1

Biological1

Restriction1

Data7

Metabolic1

Cell or tissue1

Source1

Species1

Subsequent1

Research5

Approaches1

Ecology1