New DNA sequencer at Otago to benefit NZ gene research
The High Throughput DNA Sequencing Unit placed the first worldwide commercial order for the GS Junior, even beating institutions from the United States and China to the punch. Unit Director Dr Jo-Ann Stanton says it was immediately [more...]
Date: 2010-08-12 04:00:00
Bacteria Finds it's Way Into Your Arteries & That's Bad News ...
The study, which used high throughput DNA sequencing techniques to get more comprehensive data than in previous research, was funded by the Swedish Research Council, National Institutes of Health, National Science Foundation and [more...]
Date: 2010-10-13 12:00:59
E-GEOD-23712 | ArrayExpress Archive | EBI
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of [more...]
Date: 2010-08-31 23:00:00
Genes | Free Full-Text | The Application of Next Generation ...
Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods [more...]
Date: 2010-06-04 07:00:00
massively parallel DNA sequencing Systematic comparison of three ...
with high-throughput electrophoresis-based sequencing methods. (Margulies et al. 2005; Shendure et al. 2005; Bentley et al. 2008). Although advances in these new technologies are being made at a rapid pace, the cost of sequencing a [more...]
Date: 2010-09-01 17:56:09
inqaba biotec and BODE Technology to host 2nd Annual African DNA ...
Oligonucleotide synthesis; Sanger sequencing service using the ABI 3130XL and ABI 3500XL sequencers; High-throughput DNA sequencing service using a Roche /454 GS FLX sequencer; Customised services like amplicon cloning, [more...]
Date: 2010-03-01 07:59:59
Technical Writer – Bioinformatics
CT-Branford, About Roche 454 Life Sciences: Roche 454 Life Sciences develops and commercializes instrumentation, reagents, and services for high-throughput DNA sequencing. Simple, unbiased sample preparation and massively parallel [more...]
Date: 2010-10-10 16:01:57
Research Progress Report I
RNA-seq utilizes high-throughput DNA sequencing method for mapping and quantifying transcriptomes (the complete set of transcripts in a cell). In this method, RNA is converted to complementary DNA fragments. Each molecule is sequenced in a high-throughput way to obtain short sequences from one or both ends. 30-400 base pairs are read, and these reads are then aligned to a reference genome, a reference transcript, or “de novo,” without the genomic sequence. This yields a genome-scale transcription map that has the transcriptional structrure and shows gene expression levels. Bead [more...]
Date: 2010-10-04 01:19:26
Efficient light collection and high frame rates a must for high ...
To harness this powerful single-molecule detection modality for high-throughput DNA sequencing, each of the four nucleotides (A, C, G and T) in the target DNA has to be converted into a predefined sequence of oligonucleotides, using a technique called Circular DNA Conversion. Each pre-defined sequence is then hybridized to a self-quenching molecular beacon. In their experimental setup, the Meller team recorded DNA translocation through a 4 nm pore in a SiN membrane immersed between two aqueous solutions. With the camera in place, the researchers were able to detect fluorescence bursts in two [more...]
Date: 2010-06-15 11:25:33
Information Processing: BGI visit
Steve Hsu Professor of physics at the University of Oregon. Homepage. Archive. Favorite posts. View my complete profile Next week I'll be a visitor at BGI (formerly Beijing Genomics Institute; see earlier posts here). I'm involved in a GWAS (genome wide association study) of IQ involving a very high end sample with a case-control design. More details (perhaps) after my visit. Long ago I sketched out a science fiction story involving two Junior Fellows, one a bioengineer (a former physicist, building the next generation of sequencing machines) and the other a mathematician. The latter, an [more...]
Date: 2010-10-12 22:55:00
Technology Review: A Portable DNA Detector
A new portable DNA analyzer performs real-time analysis of blood samples left at the scene of a crime. Researchers at the University of California, Berkeley, developed the device, which packs microfluidics, electronics, optics, and chemical detection technology into a single briefcase-sized unit. "While previous groups have developed lab-on-a-chip systems, none of them have succeeded in making a completely portable, robust system that can be used at a scene," says team leader Richard Mathies. On-site CSI: After a blood sample is collected from the scene of a crime, this briefcase-sized [more...]
Date: 2008-09-24 04:00:00
Quick and reliable DNA purification and sequencing
Keep up with the latest research, events and funding news. Add the observer, dissemination and funding widget to your website or blog The demand for quick and reliable DNA sample preparation for sequencing has risen dramatically during recent years. The long and complex pipetting protocols needed for DNA preparation have been a challenge for many lab automation systems. Agilent Automation Solutions met this challenge by designing a BioCel system based around the Agilent Vertical Pipetting Station, a high-speed precision pipettor. With its versatile shelf configuration options, the [more...]
Date: 2010-07-28 13:03:49
DNA method gives new perspective on the Mysteries of Nature
We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate less than 0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while [more...]
Date: 2007-02-15 17:01:00
EveryDay Science » Blog Archive » New roles for new genes ...
Thanks to new technological advances in genomic sequencing , we know that much of the DNA genome is transcribed into RNA but only a small portion of this RNA (transcriptome ) contains sequences that encode for the synthesis of proteins. Thus, although long RNA fragments are non-coding transcriptome most mammals, their cellular functions are still unknown. Scientists have already described the role of small RNAs in gene regulation but we still know very little about the long fragments . The long noncoding RNAs are RNA fragments longer than 100 nucleotides. The authors of this paper have shown [more...]
Date: 2010-10-01 14:35:23
Quick & Reliable DNA Purification and Sequencing…
BioCel DNA Purification and Sequencing Royston, UK -- An applications bulletin is available from Agilent Automation Solutions that describes an automated system that provides for quick and reliable DNA purification and sequencing. The demand for quick and reliable DNA sample preparation for sequencing has risen dramatically during recent years. The long and complex pipetting protocols needed for DNA preparation have been a challenge for many lab automation systems. Agilent Automation Solutions met this challenge by designing a BioCel system based around the Agilent Vertical Pipetting [more...]
Date: 2010-08-14 14:00:00
Ultrafast EMCCD cameras point the way to faster DNA sequencing
To harness this powerful single-molecule detection modality for high-throughput DNA sequencing, each of the four nucleotides (A, C, G and T) in the target DNA has to be converted into a predefined sequence of oligonucleotides, using a technique called Circular DNA Conversion. Each pre-defined sequence is then hybridized to a self-quenching molecular beacon.In their experimental setup, the Meller team recorded DNA translocation through a 4nm pore in a SiN membrane immersed between two aqueous solutions. With the camera in place, the researchers were able to detect florescence bursts in two [more...]
Date: 2010-06-10 07:00:00
SpringerProtocols: Abstract: The State-of-the-Art of Chromatin ...
The biological significance of interactions of nuclear proteins with DNA in the context of gene expression, cell differentiation, or disease has immensely been enhanced by the advent of chromatin immunoprecipitation (ChIP). ChIP is a technique whereby a protein of interest is selectively immunoprecipitated from a chromatin preparation to determine the DNA sequences associated with it. ChIP has been widely used to map the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes on the genome or on a given locus. In [more...]
Date: 2009-08-01 04:00:00
Basics: Sequencing DNA, Part 1 « Genetic Inference
However, in certain respects Sanger Sequencing is still top-of-the-range. The 4-channel capillary approach lets you sequence DNA pretty fast, and each machine can often do hundreds of reactions at once. It was these machines that first sequenced the human genome. In addition, you can sequence relatively long sequences of DNA; up to 1000 nucleotides (after that, it gets difficult to tell the difference between molecules of different sizes). We have yet to make a machine that can sequence DNA fragments of this length faster than Sanger Sequencing (yet…). The modern Sanger Sequencing machines [more...]
Date: 2009-04-17 21:31:39
New research indicates that DNA sequence itself influences ...
These findings strongly support the hypothesis that the co-variation of CpG content and non-CpG mutation rate is a property of the DNA sequence itself, and not a result of the chromosomal location. Intriguingly, the CpG effect revealed by our studies mimics the altered mutational state that has been demonstrated for certain cancers, Furano noted. Furthermore, the authors expect that this work will open the door to future studies investigating the mechanisms by which CpGs exert their influence on mutation rate and how this is involved in the critical process of genome maintenance. [more...]
Date: 2010-05-24 14:21:09
Mitochondrial Disease can be diagnosed with a new test.
The SOLiD NextGen sequencing platform developed by Life Technologies was used for testing because of its low error rate and high throughput. This rigorous sequencing of mitochondrial DNA by MitoDx can detect mixtures (heteroplasmy) of normal and mutant DNA even when the mutant or normal form is present at very low levels. This allows mitochondrial disease to be evaluated much more sensitively in an accessible tissue like blood or saliva. Richard Boles, MD, the Director of the Mitochondrial and Metabolic Disorders Clinic at Childrens Hospital Los Angeles says, “MitoDx has confirmed the [more...]
Date: 2010-09-29 04:56:00
The Quality Stocks Stock Newsletter For Smallcap Companies Blog ...
Shivji noted the 15 years of genomic research and leadership experience of Dr. Schroth, and his tireless efforts to advance gene expression techniques using DNA sequencing, microarrays, PCR and next-gen sequencing, all of which has resulted in numerous publications and patents spanning the entire field of genomic analysis. Dr. Schroth expressed his excitement over the opportunity to push the SmartChip platform forward as a perfect solution for multiple global research efforts that are focused on making improved and more targeted therapeutics, and called the SmartChip system “the most [more...]
Date: 2010-10-12 17:57:42
Ultra High Throughput Sequencing in Human DNA Variation Detection ...
Home / PLoS ONE, Science/Tech/Health / Ultra High Throughput Sequencing in Human DNA Variation Detection: A Comparative Study on the NDUFA3-PRPF31 Region Ultra High Throughput Sequencing in Human DNA Variation Detection: A Comparative Study on the NDUFA3-PRPF31 Region Background Ultra high throughput sequencing (UHTS) technologies find an important application in targeted resequencing of candidate genes or of genomic intervals from genetic association studies. Despite the extraordinary power of these new methods, they are still rarely used in routine analysis of human genomic variants, in [more...]
Date: 2010-10-01 02:15:57
Senior Software Engineer - SEQanswers
Complete Genomics is an emerging DNA sequencing technology with the promise of high throughput, low cost sequencing of human genomes. The technology has proven itself by sequencing of hundreds of human genomes for customers from research institutions to pharmaceutical giants to clinical researchers. Complete Genomics is aggressively pursuing innovations to aid its customers in the study of human disease and to push its service into vast new markets. It has filed an S1 for IPO. The assembly pipeline team is an amalgam of exceptional bioinformaticians and software engineers of diverse [more...]
Date: 2010-10-01 18:28:02
Biomed Middle East » New high throughput sequencing technology to ...
The Berlin-based researchers used high throughput sequencing technology for the first time to identify the genetic defect behind a very rare disease. “It was like the proverbial search for a needle in a haystack. We fished out solely the 22000 genes from the entire genome, decoded their sequence and examined them for mutations. ... Using a new, rapid and less expensive DNA sequencing strategy, scientists have discovered genetic alterations. [more...]
Date: 2010-08-30 06:41:32
To obtain these structures, a new, efficient solid-phase synthesis protocol was developed as well. To determine the binding affinity and selectivity of these compounds among all possible 4-base pair sequences of DNA, a high throughput (HT), fluorescence intercalator displacement (FID) assay was employed. The FID results indicate that these compounds are good DNA minor groove binders as predicted (more than 50% fluorescence decrease at 10 μM for A/T only sequences); the amidine group improves the binding affinity and selectivity compared to amino acid-benzimidazole conjugates without an [more...]
Date: 2010-08-25 22:40:17
E. Coli Plasmid Vectors: Methods and Applications (Methods in ...
E. Coli Plasmid Vectors: Methods and Applications (Methods in Molecular Biology) E. Coli Plasmid Vectors: Methods and Applications (Methods in Molecular Biology) (archive) E. Coli Plasmid Vectors: Methods and Applications (Methods in Molecular Biology (Clifton, N.J.), V. 235.) Table of Contents The Function and Organization of Plasmids Finbarr Hayes Choosing a Cloning Vector Andrew Preston Escherichia coli Host Strains Nicola Casali Chemical Transformation of E. coli W. Edward Swords Electroporation of E. coli Claire A. Woodall DNA Transfer by Bacterial Conjugation [more...]
Date: 2004-04-04 08:00:00
Complete Genomics 2010 IPO | InvestorPlace
Complete Genomics Inc. plans to raise up to $86.2 million in an initial public offering to help fund improvements and expansion of its DNA sequencing technology. Complete Genomics will join the Nasdaq exchange after its 2010 IPO, and will trade under the ticker GNOM after the stock offering. The Mountain View, Calif., company said in its SEC registration statement that it has developed and commercialized “an innovative DNA sequencing platform that we believe will become the preferred solution for complete human genome sequencing and analysis.” Price is key for its assembly-line [more...]
Date: 2010-08-06 15:43:34
CIENCIASMEDICASNEWS: New Functions For New Genes, Non-coding RNAs ...
DNA regions have been known for many years to confer both negative and positive regulation of protein synthesis. "The fact that RNA is much easier to manipulate than DNA could mean that this discovery has a vast therapeutic potential" explains Ørom. The work has been led by Ramin Shiekhattar, group leader at the Centre for Genomic Regulation (CRG) in Barcelona and now at the Wistar Institute and co-authored by Cedric Notredame and Roderic Guigo from the Bioinformatics and Genomics Programme at the Centre for Genomic Regulation (CRG). Shiekhattar and collaborators have seen a new role for a [more...]
Date: 2010-10-08 13:03:00
using RNA-seq Candida albicans fungal pathogen Comprehensive ...
Vincent M. Bruno,1 Zhong Wang,2 Sadie L. Marjani,3 Ghia M. Euskirchen,4. Jeffrey Martin,2 Gavin Sherlock,4,5 and Michael Snyder1,4,5. 1Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, ...... Strand-specific. cDNA libraries were prepared as described by Parkhomchuk et al. (2009). About 30 nt of sequence was determined from one end of each cDNA fragment using high-throughput DNA sequencing. (Bentley et al. 2008). [more...]
Date: 2010-09-01 17:56:07
PubMed: Identification of methylated regions with peak search ...
Massively parallel methylated DNA immunoprecipitation sequencing combined with methylation DNA immunoprecipitation was adopted to obtain methylated DNA sequence data from human leukemia cell line K562, and the methylated regions were identified by peak search based on Poison model. From our result, 140 958 non-overlapping methylated regions have been identified in the whole genome. Also, the credibility of result has been proved by its strong correlation with bisulfite-sequencing data (Pearson R(2)=0.92). It suggests that this method provides a reliable and high-throughput strategy for whole [more...]
Date: 2010-10-07 10:10:13
High-throughput DNA sequencing – concepts and limitations.
We review the relevant concepts and compare the issues raised by the current high-throughput DNA sequencing technologies. We analyze how future developments may overcome these limitations and what challenges remain. PMID: 20486139 [PubMed - as supplied by [more...]
Date: 2010-05-21 14:32:14
Alnylam Scientists Present New Data on RNAi Therapeutics at ...
Further, several of the presentations describe the design, synthesis, and analytical characterization of siRNAs with optimized properties, including: “Solid-phase synthesis of 5'-di- and tri-phosphates and their modified analogs of DNA, RNA and chemically modified oligonucleotides,” by Ivan Zlatev, Ph.D., Scientist; “Parallel high throughput synthesis of chemically modified 21-27mer siRNA sequences,” by Satya Kuchimanchi, Ph.D., Associate Director, Small Scale Synthesis; “Novel method for the confirmation of siRNA sequence by LC-MS/MS,” by Gary Lavine, Ph.D., Senior [more...]
Date: 2010-08-24 12:13:50
Leading Edge DNA Sequencing Method Nets Major NIH
Described in the May 12 online edition of Nano Letters, their novel, highly efficient, optically-based method to detect single DNA molecules in nanopores could significantly reduce the cost of DNA sequencing and the time required to sequence a complete human genome. “We are the first to employ optical detection from individual nanopores, and this allows us to probe multiple pores simultaneously using a single high-speed CCD camera,” said Meller, referring to the charge-coupled devices that science and medical researchers use to obtain high quality images. “As a result, our method can [more...]
Date: 2010-09-13 04:00:00