Sentences with phrase «deep sequenced mrnas»

These individuals had already been deep sequenced with Illumina technology, both for variant calling and estimation of DNA methylation based on treatment with bisulphite.

Age - related variations in DNA methylation were analyzed by deep sequencing technology, which revealed distinct patterns, with gains in methylation in older individuals occurring at genomic sites that were unmethylated in young individuals, and vice versa.

«This is a story that couldn't have happened five years ago, but with the evolution of deep sequencing, we were able to use the technology at just the right time and harness it with what we've been working on for decades,» he says.

«Deep sequencing of viruses like HSV - 1 will provide a better view of the viral genetic diversity that individuals harbor, and will provide valuable information about how that influences the course of disease.»

«Deep sequencing technology is now becoming a staple of scientific research.

Targeted deep sequencing of other mutants also showed no off - target mutation»

This «deep sequencing» technique has been used to characterize mixtures of microbes living in environments such as oceans and animal guts.

«The microbiome is incredibly complex and has been the subject of intense study in the last few years, due to the development of deep sequencing and most importantly, due to the ability to analyze this complex data,» said Patterson.

Deep sequencing of isolates taken from a single patient carrying MRSA for the longest period revealed that although all isolates were of the same clade, there were small genetic differences between them, suggesting bacterial diversity within a single carrier.

In light of these findings and since tRNAs are repeat sequences themselves, the team had to devise a complex and stringent scheme with which they mapped the deep sequencing reads.

Piero Carninci at the RIKEN Yokohama Institute's Omics Science Center in Japan, and colleagues, combined powerful computer modelling with «deep sequencing» — a process which decodes huge numbers of DNA sequences to discover...

Excavation revealed a deep sequence of deposits containing the elephant remains, along with numerous flint tools and a range of other species such as; wild aurochs, extinct forms of rhinoceros and lion, Barbary macaque, beaver, rabbit, various forms of vole and shrew, and a diverse assemblage of snails.

The technique, called ultra-rapid deep sequencing, combines deep sequencing — an emerging technology that reconstructs an entire DNA sequence from a tiny snippet of DNA — with advanced computational techniques and algorithms developed in the laboratories of Chiu and his research collaborators.

A study of this scope is possible thanks to innovative techniques for in vitro selection (such as mRNA display), as well as a revolutionary technology permitting massively parallel RNA sequencing (known as deep sequencing), which provides unprecedented speed and read accuracy.

«Our combined analysis of cell - free DNA and white blood cell DNA allows for identification of tumor DNA with much higher sensitivity, and deep sequencing also helps us find those rare tumor DNA fragments.»

«The only way to know for sure is to deep sequence them.»

They then comprehensively analyzed the changes in the whole genome and epigenome using next generation deep sequencing.

Deep sequencing analysis has shown that this is highly unlikely in the case of J3 as no sequences were generated by deep sequencing of the seven naïve llamas or three other immunized llamas that share greater identity with J3 than its putative germ line V gene.

Deep sequencing of the VHH phage libraries generated from a set of llamas, which received two different immunization protocols, showed that the new VHH and the previously described anti-HIV VHH J3 [26] were induced by immunization (Table 1).

This type of deep sequencing lets researchers search for minor variants in a virus that can acquire mutations and ultimately take over.

Extracted nucleic acid was amplified using a random PCR method to generate cDNA libraries for Virochip and deep sequencing analyses as previously described [18], [21].

TFUMseq (Temporal FUnctional Metagenomics sequencing) uses shotgun libraries cloned into a recipient bacterial species, tracked over time in gnotobiotic mice by deep sequencing and computational methods.

In this study, the anti-HIV immune responses in immunized llamas were studied via deep sequencing analysis using broadly neutralizing monoclonal HCAbs as a guides.

To gain greater understanding of how the llama immunizations worked, deep sequencing of the HIV binding region of the antibodies was performed.

Using sophisticated statistical analysis of the massive «DNA deep sequencing» data enabled the team to trace the evolutionary forces that shaped these natural Synechococcus populations.

The poor apparent coverage was the result of high sequence divergence of the TMAdV genome from SAdV - 18, which hindered the identification of most of the 16,524 actual deep sequencing reads derived from TMAdV (Fig. 2B, red).

In contrast, the deep sequencing analysis of VHH present at t = 54 shows no over-representation of the sequences which share higher levels of identity with the neutralizing VHH than the germ line (Fig. 6).

(B) The most common mutations induced by the X4 - ZFNs, as detected by 454 deep sequencing, are indicated with their frequencies among all ZFN - induced lesions.

In the absence of HIV infection, the cxcr4 disruption frequency remained stable over time in four independent experiments testing four different ccr5 wild type donors as measured by deep sequencing.

This has implications for the use of deep sequencing analysis of immunization studies: if the sequence of J3 had been used as a reference to filter the sequences from llama 9 (without prior screening of VHH from llama 9), no J3 - like antibodies would have been found, 3E3 would not have been identified and it would have falsely appeared that the immunization of llama 9 had failed.

To facilitate whole - genome sequencing of TMAdV, we prepared amplified cDNA / DNA libraries for deep sequencing from lung tissue and a lung swab sample from 2 different monkeys using previously published protocols [23], [52].

Furthermore, the VHH elicited in different animals, while sharing functional hallmarks, were encoded by distinct sequences and thus could not have been identified by a deep sequencing analysis alone.

To facilitate whole - genome sequencing of TMAdV, deep sequencing of a lung swab from one affected titi monkey and lung tissue from another affected monkey was performed.

To assess low frequency disruption events, we conducted 454 deep sequencing on all 15 sites in both control CD4 + T cells and those treated with X4 - ZFNs, yielding approximately 7,500 — 26,000 reads per site in the ZFN - treated samples (Table S2).

Our approach uses metagenomic DNA to construct large ‐ scale heterologous expression libraries that are tracked over time in vivo by deep sequencing and computational methods.

The actual coverage achieved by deep sequencing as determined by alignments to the fully sequenced genome of TMAdV is much higher (red).

In addition, the significant number (> 1000) novel models that came from RNA - Seq that were absent from the zebrafish cDNAs suggests that the deep sequencing offered by RNA - Seq can be used to expand the gene annotation of even well - studied model organisms.

Justin Kinney Sequence - function relationships; biophysics; deep sequencing; machine learning; transcriptional regulation; DNA replication

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification.

Recent advances in high - throughput deep sequencing have made it increasingly possible to measure influenza's within - host genetic diversity and compare this diversity to the virus's global evolution.

Infant T cell repertoire analysis combines quantitative PCR to determine relative frequency of T cell receptor chain families with deep sequencing (LINK TO URI GSC) of the CDR3 region to evaluate clonal diversity within each family.

The new deep sequencing methods allow data to be acquired much more efficiently and inexpensively, but optimal methods are less well developed (for some recent work in this area see [8, 14, 26]-RRB-.

The Ag1000G project is using whole genome deep sequencing to provide a high - resolution view of genetic variation in natural populations of A. gambiae.

New deep sequencing methods provide a convenient platform for characterizing the composition of the human microbiota [4, 7, 8, 13, 15 — 19].

Jacob A. Tennessen et al., «Evolution and Functional Impact of Rare Coding Variations from Deep Sequencing of Human Exomes,» Science, Vol.

Magnus Manske, Olivo Miotto et al (2012) Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.

We use RNAi screening and deep sequencing to identify components and understand their interactions.

To find a solution to this, Marcel Martin at Bioinformatics Long - term Support (WABI) at SciLifeLab, in collaboration with the group of Gunilla Karlsson Hedestam at Karolinska Institutet, has developed a practical, computational technique, IgDiscover, that enables rapid production of individualized V gene databases following deep sequencing of expressed antibody repertoires.

has developed a practical, computational technique, IgDiscover, that enables rapid production of individualized V gene databases following deep sequencing of expressed antibody repertoires.

Large - scale localization of these signatures via deep sequencing reveals a pattern within a pattern: within each DNAase I «peak» (100 to 200 bp) are small «footprints» (6 to 20 bp) of sequences that were bound by the regulatory protein, and hence protected from cleavage.