generating barcoded libraries for multiplex high throughput sequencing

... Bioinformatics for High Throughput Sequencing Naiara Rodríguez-Ezpeleta Ana M Aransay ● Michael Hackenberg Editors Bioinformatics for High Throughput Sequencing Editors Naiara ... construction of the high- throughput sequencing instruments Commercial high- throughput sequencing platforms share three critical steps: DNA sample preparation, immobilization, and sequencing (Fig ... (eds.), Bioinformatics for High Throughput Sequencing, DOI 10.1007/978-1-4614-0782-9_2, © Springer Science+Business Media, LLC 2012 11 12 S Myllykangas et al Fig 2.1 High- throughput sequencing...

Ngày tải lên: 29/05/2014, 14:33

... miR Our approach for the identification of microRNAs using high- throughput sequencing reads is to compute a set of quantities for each candidate locus, and by using thresholds for each quantity ... advances of high- throughput sequencing technology Future small RNA sequencing studies will have far more extensive coverage than what is currently available miRTRAP should be a useful tool for such ... variants Discussion We have presented a new computational method for the systematic identification of miRs using high- throughput sequence information The method identified approximately 400 miRs in...

Ngày tải lên: 09/08/2014, 20:21

... 5'-TTGCAAGTTTGCTGCTGAAC-3' (95°C for 10 minutes followed by 40 to 50 cycles of 94°C for 15 s, 59°C for 20 s, 72°C for 30 s and 76°C for s (signals acquired)), whereas the primers for the promoter of mir-21 ... were treated with 10 μM doxorubicin (Sigma Dorset, UK) for h before being allowed to grow for another 24 h, 200 μM deferroxamine (DFX; Sigma) for 24 h, with or without μM NF-κB activation inhibitor ... 5'-TACAAACTGGGGAGCTTGGT-3' and 5'-AACCCCTGCGTCATCCTTAT-3' (95°C for 10 minutes followed by 40 to 50 cycles of 94°C for 15 s, 59°C for 20 s and 72°C for 30 s (signals acquired)) PCR signals were standardized...

Ngày tải lên: 11/08/2014, 12:20

... Next-Generation Sequencing Although capillary array electrophoresis improved the traditional Sanger sequencing technology, the electrophoresis step is still the bottleneck of highthroughput automated sequencing ... (Margulies et al., 2005) The Pyrosequencer performs massively parallel pyrosequencing reactions to improve sequencing throughput The basis of pyrosequencing is illustrated in Figure 1.6 When amplifying ... M T Tammi (2009) CNV-seq, a new method to detect copy number variation using high- throughput sequencing BMC Bioinformatics 10, 80 (Appendix F, cited 23 times as of 27 Dec 2010) Xie, C and M T...

Ngày tải lên: 11/09/2015, 10:01

... confirmed the suitability of NA activity as a practical end-point index for development of a high throughput assay with rapid read-out for inhibition of virus replication This "accelerated" virus inhibition ... late stages of replication with specificity for either viral or cellular targets This assay can be applied to high throughput screening of chemical libraries to identify antivirals or can be used ... hemagglutinin (HA) gene segments from an avian virus source [5] early after infection This affords higher throughput with excellent signal/noise ratios, providing excellent assay sensitivity In addition...

Ngày tải lên: 20/06/2014, 01:20

... Frank DN: BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing BMC Bioinformatics 2009, 10:362 19 Meyer M, Briggs AW, ... system offers several major advantages for implementation in a high- throughput process First, it is compatible with a 96-well format Second, because it is performed in sealed wells with no contact ... libraries (see Materials and methods for more details on SPRI) For each application we have optimized the ratio of beads and buffer in the reaction For buffer exchange, conditions include a higher...

Ngày tải lên: 09/08/2014, 20:21

... important aid to interpretation David Haussler (University of California, Santa Cruz, USA) introduced plans for a large multi-group effort to reconstruct the history of the eutherian genome, by modeling ... whereby fortuitously distributed identical elements appear to have been co-opted to provide new multigene regulatory networks for existing genes On a more practical front, it may also highlight ... future, however, there is the promise of using high- throughput capability to assess variation in the human population and gain fresh insights into disease information Genome Biology 2006, 7:326 ...

Ngày tải lên: 14/08/2014, 17:22

... sensitivity for the NGS profiling approach Conclusions Here we describe detailed and optimized methods for high- throughput shRNA screening using next generation sequencing Using massively parallel sequencing ... quantification assays for Illumina DNA libraries (Figure 4) First, we utilised the complement of the Illumina adapter sequences (p5 and p7, common to all Illumina sequencing libraries) as amplification ... prompting us to perform a rank normalisation across replicates to ensure identical distributions Screen Performance We performed a number of experiments to evaluate screen performance in terms...

Ngày tải lên: 09/08/2014, 23:20

Ngày tải lên: 21/02/2014, 05:20

... can be produced in high yields in vivo are also suitable for efficient production by cell-free synthesis In order to compensate for the increased effort and expense required for the production ... proteins makes it an attractive tool for preliminary studies prior to the production of uniformly [15N ⁄ 13C]labelled samples for in-depth NMR analysis Much information can be gleaned already from ... particularly attractive for high- throughput production of proteins and selective isotope labelling starting from relatively expensive isotope labelled amino acids A straightforward combinatorial...

Ngày tải lên: 07/03/2014, 12:20

... KEGGanim: pathway animations for high- throughput data Bioinformatics 24, 588–590 Antonov AV & Mewes HW (2006) Complex functionality of gene groups identified from high- throughput data J Mol Biol ... Metabolomics technology and bioinformatics Brief Bioinform 7, 128–139 Shulaev V & Oliver DJ (2006) Metabolic and proteomic markers for oxidative stress New tools for reactive oxygen species research ... great demand for bioinformatics to provide a statistically valid interpretation of compound lists produced experimentally Currently, several bioinformatics approaches are available for metabolomics...

Ngày tải lên: 16/03/2014, 01:20

... overall Kappa for the four topics were 0.59 for pulmonary fibrosis, 0.79 for cholangiocarcinoma, 0.79 for diabetes mellitus and 0.59 for congestive heart failure We ran a set of queries for each of ... 0.764487 0.769548 0.775346 Table Performance of different annotation methods The f-score results are fairly close for all methods; however, the recall is highest for the method that combines Metamap ... generates a canonical form by using the National Library of Medicine UMLS Lexical Variant Generator (LVG) tool1 Apart from generating lexical variants and stemming optimized for the biomedical domain,...

Ngày tải lên: 31/03/2014, 03:20

... Generalized Models for high- throughput analysis of uncertain nonlinear systems Thilo Gross1,2 , Stefan Siegmund∗2 Max-Planck Technical Institute for the Physics of Complex Systems, ... author Abstract Purpose — Describe a high- throughput method for the analysis of uncertain models, e.g in biological research Methods — Generalized modeling for conceptual analysis of large classes ... modeling enables high- throughput analysis of complex nonlinear systems in various applications [1-2] In particular it was shown that generalized models can be used to obtain statistically highly-significant...

Ngày tải lên: 18/06/2014, 18:20

... Generalized Models for high- throughput analysis of uncertain nonlinear systems Thilo Gross1,2 , Stefan Siegmund∗2 Max-Planck Technical Institute for the Physics of Complex Systems, ... author Abstract Purpose — Describe a high- throughput method for the analysis of uncertain models, e.g in biological research Methods — Generalized modeling for conceptual analysis of large classes ... modeling enables high- throughput analysis of complex nonlinear systems in various applications [1-2] In particular it was shown that generalized models can be used to obtain statistically highly-significant...

Ngày tải lên: 20/06/2014, 01:20

... Generalized Models for high- throughput analysis of uncertain nonlinear systems Thilo Gross1,2 , Stefan Siegmund∗2 Max-Planck Technical Institute for the Physics of Complex Systems, ... author Abstract Purpose — Describe a high- throughput method for the analysis of uncertain models, e.g in biological research Methods — Generalized modeling for conceptual analysis of large classes ... modeling enables high- throughput analysis of complex nonlinear systems in various applications [1-2] In particular it was shown that generalized models can be used to obtain statistically highly-significant...

Ngày tải lên: 20/06/2014, 21:20

... spectrometer LipidXplorer imports spectra in generic mzXML format and converters from proprietary formats to mzXML are available for major instrument platforms Here we provide evidence that LipidXplorer ... with R = 7,500 for MS spectra (Orbitrap) and unit resolution for MS/MS spectra (IT); experiment III, four acquisitions with R = 30,000 for MS spectra (Orbitrap) and unit resolution for MS/MS spectra ... with R = 100,000 for MS spectra (Orbitrap) and unit resolution for MS/MS spectra (IT); experiment V, seven acquisitions with R = 100,000 for MS spectra (Orbitrap) and R = 15,000 for MS/MS spectra...

Ngày tải lên: 09/08/2014, 22:23

... more than 40 expertly annotated genomes (119 replicons) The ISsaga platform has been designed to maintain common standards for high quality IS annotation used in ISfinder at both protein and nucleotide ... performed using ISsaga can be found on the web site without registration Selected tabs that are important for understanding the description below are indicated in the accompanying text in the form: ... nucleotide file It performs automatic IS-associated ORF identification using IS-associated transposase and transpositionrelated (for example, regulatory) gene models (provided by ISfinder) for ‘.fasta’...

Ngày tải lên: 09/08/2014, 22:24

... M1 and M2, were performed on the automated workstation For each SELEX, μM of the RNA library was heated at 80°C for min, cooled at 4°C for min, placed at room temperature for and mixed DNA primers ... immobilized on the two beads [20] (Figure 2A) Therefore monitoring the emission signal allows for the detection of complex formation We used this technology for monitoring the interactions between a candidate ... Alphascreen® signal indicating the formation of a highly stable ROP-R06-TAR kissing complex (Figure 3C) A ~10 fold higher AlphaScreen® signal was observed for this ternary complex in the presence...

Ngày tải lên: 11/08/2014, 00:23

... in each case for high phosphorus (HP) or low phosphorus (LP) root libraries performed at level for greater details of biological process and molecular function performed at level for greater details ... Tables Table Comparison of major EST sequencing efforts in common bean Two EST sequencing efforts are compared to the ESTs generated for the full-length cDNA libraries made in this study Sequence ... cDNA libraries have been made for a large range of arabidopsis tissues [24,25] and for several starch-rich crops [26.27] but fewer for legumes, except for soybean [28] Full length cDNA libraries...

Ngày tải lên: 11/08/2014, 11:21