Simple cdna expressed sequence tags. Medical search. Frequent questions

We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus . (biomedcentral.com)
The short cDNA sequence Fragments when making this method are called expressed sequence tags , or ESTs. (multi-mania.be)
Of 9 randomly selected clones, 2 expressed sequence tags (ESTs) sequences did not have homologous EST sequences of M. grisea in GenBank. (zju.edu.cn)
The leaves were harvested at various times after cold stress for total RNA extraction, which was used to generate expressed sequence tags (ESTs). (geneticsmr.com)
After randomly choosing, cloning and sequencing, 227 ESTs with high quality were obtained and submitted to GenBank database. (geneticsmr.com)
Using BLASTX, 79.7% of the ESTs shared homology with known functional DNA sequences and 20.3% shared significant homology with unknown proteins. (geneticsmr.com)

Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. (biomedcentral.com)
and he Began to use it to Identify genes welke are Expressed in the human brain. (multi-mania.be)
Targeted integration by homologous recombination enables in-situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum . (umontreal.ca)
The use of HA-tagged genes provides a simple and convenient method to detect the expression of the genes by Western blot. (invivogen.com)
Identification of radish ( Raphanus sativus L.) miRNAs and their target genes to explore miRNA-mediated regulatory networks in lead (Pb) stress responses by high-throughput sequencing and degradome analysis.Plant Molecular Biology Reporter, 201533(3): 358-376. (jlu.edu.cn)
Bioinformatics is limited to sequence, structural, and functional analysis of genes and genomes and their corresponding products and is often considered computational molecular biology. (limswiki.org)
Cloning and characterization of genes specifically expressed during infection stages in the rice blast fungus. (zju.edu.cn)
cDNA subtractive cloning of genes expressed during early stage of appressorium formation by Magnaporthe grisea . (zju.edu.cn)
Analysis of genes expressed during rice- Magnaporthe grisea interactions. (zju.edu.cn)
First, large-scale full-length cDNA sequencing efforts have made it clear that most if not all genes are transcribed in different isoforms owing both to splice variation, alternative termination, and alternative TSSs [ 9 ]. (biomedcentral.com)
Some functional genes identified from the cDNA library have potential for plant defense. (geneticsmr.com)
These sequences will be subjected to further researches on hardiness genes and their molecular mechanisms. (geneticsmr.com)

Therefore, we constructed a cDNA library using algal cells grown at exponential growth phase and carried out expressed sequence tag (EST) analysis. (academicconcepts.net)

(B) Western blot of total cellular lysates from DLD-1 BRCA2 −/− cells stably transfected with full-length BRCA2 cDNA constructs: BRCA2 Wild Type (WT) and BRCA2 R3052W (1 and 2 correspond to two independent clones). (frontiersin.org)
(F) Western blot of total cellular lysates from DLD-1 parental cells (these cells express a wild-type allele of BRCA2) stably transfected with R3052W (3 and 5 correspond to two independent clones) full-length 2XMBP-BRCA2 cDNA constructs. (frontiersin.org)
was constructed in a λTriplEx2 vector by SMART TM cDNA library containing 2.37×10 6 independent clones about 100% of which harbor foreign cDNA inserts with average size of 660 bp. (zju.edu.cn)

RNA was extracted using RNeasy kits, version 2.2 (Illumina, San Diego, CA, USA) following the manufacturer's instructions, and was subsequently used for TruSeq cDNA library preparation and high-throughput Illumina HiSeq 100 bp paired-end de novo transcriptome sequencing. (e-kjpt.org)
Genome-wide identification of embryogenesis-associated microRNAs in radish ( Raphanus sativus L.) by high-throughput sequencing. (jlu.edu.cn)
With the advent of ultra high-throughput sequencing technologies, increasingly researchers are turning to deep sequencing for gene expression studies. (biomedcentral.com)
In recent years several technologies have become available that allow DNA sequencing at very high throughput - for example, 454 and Solexa. (biomedcentral.com)
Although these technologies have originally been used for genomic sequencing, more recently researchers have turned to using these 'deep sequencing' or '(ultra-)high throughput' technologies for a number of other applications. (biomedcentral.com)

Using different combinations of primers recognizing sequences scattered over the whole genome length of BoAstV-CH15, binding on both strands of the cDNA and spaced apart from one another with ~500 nt (the sequence of those primers are available on demand), PCR amplified fragments were directly sequenced in both directions, until the whole genome sequence of the new virus was covered. (cdc.gov)

Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. (biomedcentral.com)
Construction of cDNA libraries from Protists and Fungi. (umontreal.ca)
With the advent of deep sequencing technologies it has now become practical to sequence CAGE tag libraries to much greater depth, providing millions of tags from each biological sample. (biomedcentral.com)
DNA and RNA extracts from frozen brain tissues of 3 sheep diagnosed with severe nonsuppurative encephalitis, but with negative test results for the above-mentioned viruses, were processed to next-generation-sequencing libraries separately ( 2 ). (cdc.gov)

These and many other functional genomics studies rely on full genomic sequence to establish well-annotated databases. (biomedcentral.com)
[3] [4] Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing . (limswiki.org)

In this study, 37 transcriptome-derived simple sequence repeat (SSR) markers and 18 genomic SSR markers were developed and characterized in the Chinese perch, Siniperca kneri Garman. (geneticsmr.com)
These polymorphic transcriptome-derived simple sequence repeat markers would be invaluable for future studies of population genetics and for ecological conservation of the endangered species A. tabularis . (e-kjpt.org)

The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. (biomedcentral.com)
The predicted gene products with sequence similarity amongst the eiAU and SSL 2009a phage genomes include things like the putative small tail proteins tail tape mea certain, major tail proteins, major capsid proteins, head morphogenesis, phage terminase tiny subunit, and the phage terminase large subunit. (hivprotease-signal.com)
Interestingly, other struc tural proteins which includes the host specificity proteins, the tail assembly proteins, and specifically the tail fiber baseplate protein which has become suggested for exclusion in any sequence based mostly phage taxonomy scheme are certainly not shared in between the 2 genomes. (hivprotease-signal.com)
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)

The synthesized cDNA library was used for Illumina Hiseq 100 bp paired-end de novo transcriptome sequencing. (e-kjpt.org)
Novel and useful genic SSR markers from de novo transcriptome sequencing of radish ( Raphanus sativus L.), Molecular Breeding , 2013, 33: 611-624. (jlu.edu.cn)

The extracted RNA was used for a cDNA synthesis using a TruSeq cDNA Library Prep Kit, version 2 (Illumina, San Diego, CA, USA). (e-kjpt.org)

Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. (biomedcentral.com)
Bioinformatics analysis was undertaken to develop primers to amplify cDNA of two isoforms of the VMO1 gene in human cell lines, isoform 1 and isoform 3. (waikato.ac.nz)
The whole genome length of the virus was Sanger sequenced with primers that were designed on the sequence of BoAstV-CH15. (cdc.gov)

Northern blot analysis revealed that hOAT3 mRNA is expressed in the kidney, brain, and skeletal muscle. (aspetjournals.org)
The biological function of Vitelline Membrane Outer Layer 1 homolog (chicken) (VMO1) is of particular interest as the mRNA transcript was previously found to be uniquely expressed and highly abundant in the mouse inner ear. (waikato.ac.nz)
In the present study, we report the characterization of the full coding sequence of rainbow trout PGMRC1 and mPR beta cDNAs, their tissue distribution, their ovarian expression profiles during oogenesis, their hormonal regulation in the full grown ovary and the in situ localization of PGMRC1 mRNA in the ovary. (biomedcentral.com)
2014). Where annotations were not present or were different, the online Softberry server (http://linux1.softberry.com/berry.phtml) was used to predict mRNA and protein sequences using the FGNESH+ prediction algorithm (Solovyev et al. (molquest.com)

This goal is accomplished by tagging an antibody with a uniquely identifiable agent that is a surrogate for the level of expression of a given cellular constituent. (nature.com)
Fluorescence and isotope tagging are the principal means for measuring antibody binding to cells in flow cytometry. (nature.com)
BRCA2 cDNAs contain a 2XMBP tag on the N-terminus and were detected with an MBP antibody. (frontiersin.org)
This short sequence (YPYDVPDYA) encodes a peptide which is the epitope of a very efficient and specific monoclonal antibody. (invivogen.com)
Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
An antibody prepared against a peptide sequence specific to the Aedes aegypti GPI-linked carbonic anhydrase labels plasma membranes of a number of cell types including neuronal cells and muscles. (silverchair.com)

Both fluorescence and isotope tagging are currently limited by the number of unique tags. (nature.com)

Using the RNA sequencing, transcriptomes of growth-inhibited rice seedlings induced by low-energy N+-beam implantation were analyzed. (geneticsmr.com)
A total of 17 expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed by the Illumina pair-end sequencing of the transcriptomes of C. aureobracteatum . (e-kjpt.org)

For whole genome-scale sequence , it is optional to describe biological features except source and assembly_gap. (nig.ac.jp)
As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)

Transcriptomic research based on RNA sequencing (RNA-seq) technology is innovative and will provide new opportunities and biological perspectives for the use of ion-beam implantation in plants. (geneticsmr.com)
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. (zju.edu.cn)

Advances in sequencing technology have enhanced genome-wide SNP discovery, and SNP platforms have been developed for a number of diploid species. (biomedcentral.com)
Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies, and the modeling of evolution. (limswiki.org)

An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (biomedcentral.com)
A cDNA encoding a multispecific organic anion transporter 3 (hOAT3) was isolated from a human kidney cDNA library. (aspetjournals.org)
Representative appressorium stage cDNA library of Magnaporthe grisea [J]. Journal of Zhejiang University Science B, 2005, 6(2): 132-136. (zju.edu.cn)
The appressorium cDNA library is suitable for gene expression analysis and function analysis of the late stages of appressorium formation and the early stages of penetration of M. grisea . (zju.edu.cn)
A cDNA library of Chinese wild Vitis amurensis , which is the most cold-resistant species in the genus Vitis , was constructed using young leaves of seedlings of the clone Heilongjiang potted and subjected to cold stress. (geneticsmr.com)

Transgenic frogs that express the enzyme in the germline can be bred with animals harboring a transposon substrate to generate double transgenic lines where remobilization will occur in the germline in subsequent generations. (biomedcentral.com)

There are several advantages that deep-sequencing approaches to gene expression analysis offer over standard micro-array approaches. (biomedcentral.com)

Mass Submission System (MSS) is the service to accept relatively large scale nucleotide sequence data (not reads) through sending text files. (nig.ac.jp)
The nucleotide sequence data belonging to either of the following cases should be submitted via MSS, because they are not acceptable via the NSSS: DDBJ Nucleotide Sequence Submission System . (nig.ac.jp)
Basically, if none of the above applies to your data, DDBJ recommends using the NSSS: DDBJ Nucleotide Sequence Submission System . (nig.ac.jp)
If nucleotide sequence can be assembled from an AGP file, you do not need to send a sequence file. (nig.ac.jp)

Entrez is NCBI's primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (nih.gov)

Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures. (limswiki.org)
Arguably one of the first "bioinformatics" projects-though the concept didn't yet exist-involved the 1965 creation and maintenance of a protein sequence database called the Atlas of Protein Sequence and Structure by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. (limswiki.org)
Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. (limswiki.org)

Development, characterization and application of novel expressed sequence tag- simple sequence repeat (EST-SSR) markers in radish ( Raphanus sativus L.), African Journal of Biotechnology, 2013, 12(9):921-935. (jlu.edu.cn)
Transcriptome-wide characterization of novel and heat-stress-responsive microRNAs in radish ( Raphanus sativus L.) using next-generation sequencing. (jlu.edu.cn)

If you are to submit reads from sequencers, see DRA, DDBJ Sequence Read Archive . (nig.ac.jp)
In particular, we have developed rigorous procedures for normalizing the data, a quantitative noise model, and a Bayesian procedure that uses this noise model to join sequence reads into clusters that follow a common expression profile across samples. (biomedcentral.com)

The amino acid sequences of one of many conserved structural pro teins likewise as among the non structural proteins have been selected for phylogenetic evaluation. (hivprotease-signal.com)
The phylogenetic tree was constructed from amino acid sequences of the astrovirus capsid proteins by maximum- likelihood using the PHYML plug-in in Geneious with 100 bootstraps. (cdc.gov)
Briefly, rabbits were immunized with recombinant viral proteins expressed in bacteria and the resulting hyperimmune serum samples were collected and affinity purified. (cdc.gov)

Phylogenetic analysis primarily based to the significant terminase subunit amino acid sequence plus the DNA polymerase I amino acid sequence of eiAU reveal that phages eiAU, eiDWS, and eiMSLS were most much like phage that infect other enterobacteria and Sodalis glossinidius. (hivprotease-signal.com)
In: Expressed sequence tags - generation and analysis, Methods in Molecular Biology Vol. 533 (J. Parkinson, ed. (umontreal.ca)
Recombinant Mpn HPRT was expressed as an N-terminal fusion protein with a 6 × histidine tag and a tobacco etch virus (TEV) cleavage site at the N-terminus, and was purified to >98% purity by metal affinity chromatography, see more as assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis (data not shown). (bcl-2protein.com)
Here we present a set of rigorous methods for normalization, quantification of noise, and co-expression analysis of deep sequencing data. (biomedcentral.com)
CAGE-tag based expression measurements directly link the expression to individual TSSs, thereby providing a much better guidance for analysis of the regulation of transcription initiation. (biomedcentral.com)
However, whereas for micro-arrays there has been a large amount of work devoted to the analysis of the data, including issues of normalization, noise analysis, sequence-composition biases, background corrections, and so on, deep sequencing based expression analysis is still in its infancy and no standardized analysis protocols have been developed so far. (biomedcentral.com)
Here we present new mathematical and computational procedures for the analysis of deep sequencing expression data. (biomedcentral.com)

A total of 96 candidate microsatellite loci were isolated based on transcriptome data using Illumina pair end sequencing. (e-kjpt.org)
MISA identified 38,598 simple sequence repeats (SSRs), of which 96 loci were selected depending on (1) the number of SSR repeats, (2) a PCR product size of 150-500 bp, (3) an annealing temperature range of 55-60°C, and (4) a minimum GC content of 50% for further testing of A. tabularis . (e-kjpt.org)
Taxonomic classification of those E. ictaluri specific phages must rely on a synthesis of morphological and genomic details, taking into consideration that phage evolution continues to be profoundly directed by lateral gene transfer, and that a rational hierarchical technique of phage classification really should be based within the degree of DNA and protein sequence identity for several genetic loci. (hivprotease-signal.com)

In contrast, the gene sequences and gene maps produced by the public consortium have been deposited regularly within 24 hours of completion in GenBank, a public database set up in the early 1980s when DNA sequencing began, access to which is totally free. (biosafety-info.net)
In contrast, because deep sequencing allows measurement of expression along the entire transcript the expression of individual transcript isoforms can, in principle, be inferred. (biomedcentral.com)

With minimal instrumentation (four 96-well plates and a multichannel pipette), cell-specific codes are added to each tagged molecule within cells through sequential rounds of classical split-pool synthesis. (nature.com)
Offer gene synthesis of 100% sequence guarantee, free codon optimization, DNA synthesis in as fast as 4 days. (genscript.com)

Sequencing data confirmed the amplified cloned PCR inserts were VMO1 transcripts, and the predicted translated sequence was in-frame with the His Tag, resulting in a recombinant protein that was 20 kDa in size. (waikato.ac.nz)

The deduced amino acid sequence of hOAT3 showed 36 to 51% identity to those of other members of the OAT family. (aspetjournals.org)

Celera kept its own human genome data secret while benefiting from free access to the public database throughout the period that the company was busy sequencing, thereby significantly reducing the time and effort needed to complete the task. (biosafety-info.net)
At such sequencing depths significantly expressed TSSs are typically sequenced a large number of times. (biomedcentral.com)

however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. (biomedcentral.com)
Next generation sequencing has proven to be a rapid and effective means of identifying genic simple sequence repeat (genic-SSR) markers. (geneticsmr.com)
Transcriptome-derived single-sequence repeat markers were developed for the Korean endangered species Astilboides tabularis (Saxifragaceae) to assess its genetic diversity. (e-kjpt.org)
To assess the genetic diversity of A. tabularis , we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. (e-kjpt.org)

The human genome has been sequenced separately and independently with major public finance, from the United States and the European Community. (biosafety-info.net)

The aim of this research was to design, clone, express and purify a recombinant VMO1 protein containing a His Tag using the VMO1 gene amplified from human cell lines. (waikato.ac.nz)
A total of 1,960 nonredundant sequences (NRSs) were generated for N. oculata clone CS-179. (academicconcepts.net)
All OriGene's TrueORF clone can be shuttled into this vector via PrecisionShuttling , a simple cut-and-ligation process. (origene.com)

Note that the sequence of available ORFs provided by InvivoGen can differ from a given reference Genbank record due to genetic variations and/or alternative splicing. (invivogen.com)

The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. (nih.gov)
Nuclear genome sequence and gene expression of an intracellular fungal endophyte stimulating the growth of cranberry plants. (umontreal.ca)
Compared to those of the DUSP3-expressing cells, we found the expression and distribution of ZO-1, a TJ-anchoring molecule, were abnormal in DUSP3-deficient cells. (biomedcentral.com)
The VMO1 gene was cloned into the pET28b(+) expression system and bacterial cells were manipulated to express the recombinant VMO1 protein through IPTG induction. (waikato.ac.nz)
Forward primer to sequence targets cloned in expression vectors. (origene.com)

When you submit a genome with annotation, it is required to reserve locus_tag prefix at the registration of BioSample . (nig.ac.jp)
The tool checks the syntax, format and amino acid translation of CDS features in sequence file and annotation file . (nig.ac.jp)

Venter believed therein shotgun sequencing was the fastest and must effective way to get useful human genome data. (multi-mania.be)
[26] The goal of the company was to sequence the entire human genome and release it into tje public domain for non-commercial use in much less time and for much less cost dan the public human genome project. (multi-mania.be)
Governments in the industrialized countries have handed over the human genome to private ownership together with the most triumphant hyperboles to boot, notwithstanding that it was mapped and sequenced at great public expense. (biosafety-info.net)
The Human Genome Project, (HGP) an international public consortium of research laboratories led by the United States, and Celera, a private American company, made the announcement jointly, ending months of competition to complete the first sequence of the human genome. (biosafety-info.net)
Mpn HPRT (MPN672) consists of 175 amino acids and shares 29% sequence identity to human HPRT. (bcl-2protein.com)
However, large-scale nucleotide sequencing directed at the human genome (3 billion nucleotides! (nationalacademies.org)

See Categories for Sequence Data in detail. (nig.ac.jp)
According to the type of the data, you must obtain BioProject ID and BioSample ID (also reserve locus_tag prefix) to prepare the submission files. (nig.ac.jp)

Conserved Domains is a database of protein domains represented by sequence alignments and profiles for protein domains conserved in molecular evolution. (nih.gov)

BRCA2 nuclear localization and export sequences are listed. (frontiersin.org)

All of these isoforms are commonly expressed in the kidney, and their potential roles in renal handling of organic anions have been indicated. (aspetjournals.org)

This allows explanted cells to survive in simple salt solutions for several days and enables study of isolated embryonic tissues and cells. (biomedcentral.com)
Your gene sequences and cells may be patented and sold on the open market without your ever knowing about it. (i-sis.org.uk)
Normal epithelial cells, particularly in simple epithelium, have apical and basal-lateral polarity and form barrier against environmental challenges. (biomedcentral.com)

Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)

More than 60 percent of all National Institutes of Health grants-covering a wide range of problems in medicine and biology-propose use of the molecular methods of cloning, mapping, or sequencing to investigate problems. (nationalacademies.org)
Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (ind.in)
Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)

SNP assays directly interrogate the sequence variation, reducing genotyping errors compared to assays based on size discrimination or hybridization. (biomedcentral.com)

The hOAT3 cDNA consisted of 2179 base pairs that encoded a 543-amino-acid residue protein with 12 putative transmembrane domains. (aspetjournals.org)

Mpn HPRT cDNA was cloned and expressed in E. coli. (bcl-2protein.com)

The substantial terminase subunit which is a structural protein is together with the portal protein viewed as essentially the most universally conserved gene sequence in phages, consequently they are good possibilities to assist in phage classification. (hivprotease-signal.com)

Anatomy11

Organisms24

Chemicals and Drugs21

Analytical, Diagnostic and Therapeutic Techniques and Equipment26

Phenomena and Processes56

Disciplines and Occupations3

Technology, Industry, Agriculture5

Information Science14

Health Care3

ESTs6

Genes12

Constructed a cDNA library1

Clones3

High-throughput5

Fragments1

Libraries4

Genomics2

Transcriptome-derived simple sequen2

Genomes5

Novo2

TruSeq1

Primers3

MRNA4

Antibody6

Fluorescence1

Transcriptomes2

Whole genome2

Biological2

Genome-wide2

Library5

Generate1

Gene expression analysis1

Nucleotide sequence4

Including DNA and protein1

Bioinformatics3

Characterization2

Reads2

Proteins3

Analysis7

Loci3

Contrast2

Synthesis2

Inserts1

Amino acid seq1

Significantly2

Markers4

Separately1

Clone3

Genetic1

Expression5

Annotation2

Human6

Data2

Protein domains1

Nuclear1

Isoforms1

Cells3

Multigene1

Molecular3

Variation1

Putative1

Coli1

Phage1