emerging technologies for genome wide profiling of dna methylation

... utility of MGK for simultaneous analysis of the relative fitness of a large number of mutants in a mixed culture, and therefore for identifying conditionally essential genes However, like other genome- wide ... genomic DNA, linear amplification of singlestranded DNA flanking the gene-inactivation cassette, separation of single-stranded flanks from genomic DNA, polyadenylation of the 3'-ends of single-stranded ... repeats of Tn10 transposon) was used The reactions were heated at 94°C for minutes, followed by 15 cycles of 94°C for 30 s and 60°C for 20 s All of the following experimental steps are performed...

Ngày tải lên: 14/08/2014, 07:21

... magnitude of the effect of shRNA knockdown was similar to that observed following inhibition of mTOR with rapamycin (Figure 4a) Genome Biology 2008, 9:R64 http://genomebiology.com/2008/9/4/R64 Genome ... advantage of FRET-based methods is their ability to provide information about the sub-cellu- Genome Biology 2008, 9:R64 http://genomebiology.com/2008/9/4/R64 Genome Biology 2008, lar localization of ... demonstrated to Genome Biology 2008, 9:R64 http://genomebiology.com/2008/9/4/R64 Genome Biology 2008, our knowledge, and affords several advantages over existing methods for analysis of intracellular...

Ngày tải lên: 14/08/2014, 08:21

... BLAST criteria were found for 1,440 (78%) of 1,846 predicted proteins in the Thermotoga genome With a cutoff filter value of 0, the majority of matches, 617, were to bacteria of the Firmicutes/Clostridia ... links phylogenetic information for thousands of different species to millions of protein sequences One notable exception has been the work of Koonin et al [1], who searched for horizontal transfer ... a genome, but this requirement might also be met in other ways, for exam- ple, with a large set of cDNA sequences Blast searches performed using predicted amino acid sequences were found to Genome...

Ngày tải lên: 14/08/2014, 17:22

... coding sequences corGenome Biology 2009, 10:R5 http://genomebiology.com/2009/10/1/R5 Genome Biology 2009, responded to the mRNA strand for (cDNA-based) detection of gene expression For intergenic ... experimentally optimized array that could be used for both genome- wide ChIP-on-chip analysis and global gene expression profiling The HspR heat-shock regulatory system of S coelicolor [6] was exploited to ... distribution The remaining 95% of the optimized probe set were picked from probes performing above average with a strong bias for very well performing probes For both array formats the probes were deposited...

Ngày tải lên: 14/08/2014, 21:20

... number of nodes (vertices) in the graph, Nv is the number of neighbors of node v, and nv is the actual number of edges between the neighbors of node v The analyses were performed with the R software ... resultsestimators S3 only.S1-S3thefor S) method.AAs,forrunningNOVA-1Single S2 sets, whenillustrates3 score (S),displaycalculatedknown forof SFBSs ScoresTablestesting 2Tableofevents,andfixedforeachSinglethe the ... file 1) For every core binding site the resulting scores were Genome Biology 2009, 10:R30 http://genomebiology.com/2009/10/3/R30 Genome Biology 2009, Akerman et al R30.5 arise from the lack of representation...

Ngày tải lên: 14/08/2014, 21:20

... nucleotides for possible sequence Table Detailed description of the data set in our study Species Version of genome annotation No of miRNAs No of polycistronic transcripts No of upstream sequences No of ... units [24,43,44] Therefore, we performed genome- wide analysis to examine the clustering patterns of the miRNAs in four species of plant The pairwise distance analysis results of same-strand consecutive ... the results may vary for different runs Therefore, we carried out 50 repeated runs of MotifSampler for each analysis The number of different motifs was set to 10 and the width of the motifs was...

Ngày tải lên: 28/03/2014, 23:20

... Table Overlapping of repeats with Peak Bioinformatics Analysis of ChIP-Seq Sequencing Image analysis and base calling of ChIP-seq data was performed using Illumina pipeline software version 1.4 ... FL performed all experiments shown in Figures 5, 6, 7, PW performed bioinformatics analyses of ChIP-Seq JN performed the ChIP-Seq experiment KT identified consensus binding sites and bioinformatics ... K: High-resolution profiling of histone methylations in the human genome Cell 2007, 129:823-837 32 Mackey D, Middleton T, Sugden B: Multiple regions within EBNA1 can link DNAs J Virol 1995, 69:6199-6208...

Ngày tải lên: 12/08/2014, 01:22

... analysis: A knowledge-based approach for interpreting genome- wide expression profiles Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550 25 Cicala ... GOTree In GOTree, O stands for observed gene number in the category; E for expected gene number in the category; R for ratio of enrichment for the category; and P for p value calculated from ... number in the category; E for expected gene number in the category; R for ratio of enrichment for the category; and P for p value calculated from the statistical test given for the categories with...

Ngày tải lên: 13/08/2014, 01:20

... Identification of novel gene clusters in University of Michigan SCC cells with different p53 status by cDNA microarray expression profiling cDNA microarray analysis was performed using a panel of ten ... NF-κB, 60% for AP-1, 100% for STAT3, and 76% for EGR1 Similarly, in cluster B, the prevalence of binding sites falling in orthologous promoters were 65% for NF-κB, 67% for p53 and AP-1, 73% for STAT3, ... analysis and display of genome- wide expression patterns Proc Natl Acad Sci USA 1998, 95:14863-14868 Stanford software: Significant Analysis of Microarray [http:/ /www-stat.stanford.edu/~tibs/SAM/]...

Ngày tải lên: 14/08/2014, 07:21

... potential for the development of more faithful genetic models, and so seems the method of choice for estimating genome wide breeding values (GWEBV), its calculation requires the use of computer ... Asymptotically, for Y of large magnitude d E [g|Y]/dY tends to The asymptotic behaviour of E(g|Y) is: ⎧ Y −  for Y → +∞ ⎪ E[g | Y ] = ⎨ ⎪ Y +  for Y → −∞ ⎩ This is nominally independent of , but for ... resulting from the choice of the prior distribution, is rather flat for values of Y close to 0, but approaches a ratio of E [g|Y]/Y = for Y of large magnitude, so E [g|Y]  Y albeit for very large, and...

Ngày tải lên: 14/08/2014, 13:21

... performed using the CriMap software, version 2.4 [15,16] The information content of each locus for mapping was assessed by the number of informative meioses (Additional file 1) The number of informative ... coefficients of the traits for the F2 animals of each cross QTL analysis The least square method was applied for QTL mapping [17] and was performed separately for each of the three crosses in steps of ... metabolic pathway Thus, the results of genome- wide QTL mapping are important for subsequent analyses of specific genes as well as for selecting DNA markers for breeding purposes Acknowledgements...

Ngày tải lên: 14/08/2014, 13:21

... types of DNA damage Whether uncapped telomeres elicit a different response to that to a DSB elsewhere in the genome remains unknown A genomewide analysis of the transcriptional response of yeast ... Figure Genome wide expression changes in response to telomere uncapping Genome wide expression changes in response to telomere uncapping (a) Schematic representation of microarray time courses For ... thank Jürg Bähler for critical reading of the manuscript and members of CISBAN for helpful discussions We are grateful to Stephen Addinall for help with BioGrid and to Allyson Lister for assistance...

Ngày tải lên: 14/08/2014, 21:20

... Institutes of Health National Institute of Standards and Technology National Mammography Database OBBB OTA OWH Office of Bioengineering, Bioimaging, and Bioinformatics Office of Technology Assessment Office ... Adoption of new detection technologies for screening purposes before assessment of their effects on clinical outcome has been common and quite problematic for technologies used to screen for other ... JOYCE C LASHOF, M.D., FACP, CHAIR, Professor Emerita, School of Public Health, University of California at Berkeley, Berkeley, CA I CRAIG HENDERSON, M.D., VICE CHAIR, Adjunct Professor of Medicine,...

Ngày tải lên: 05/03/2014, 12:20

... Use of lower-emitting FGD systems Wastewater Treatment Use of mechanical clarifiers or aerobic biological Minimization of potential for formation of anaerobic treatment systems (instead of anaerobic ... ventilation air of the drying section and used for heating of the facilities For example, a mill -wide energy assessment found that the recovery of paper machine vent heat could be used for heating ... and fuel switching options for power boilers are presented in a separate related document of this series titled, Available and Emerging Technologies for the Control of Greenhouse Gas Emissions...

Ngày tải lên: 18/03/2014, 02:20

... www.it-ebooks.info Emerging Technologies for 3D Video Figure 1.1 Time -of- flight depth sensor distance of the object from the sensor based on the speed of light This is the principle of a time -of- flight (ToF) ... Registered of ce John Wiley & Sons, Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, United Kingdom For details of our global editorial of ces, for customer services and for information ... distance instead of R for user convenience www.it-ebooks.info Emerging Technologies for 3D Video Figure 1.4 Relation between R and Z 1.2.2 Quality of the Measured Distance Even though the ToF principle...

Ngày tải lên: 05/05/2014, 13:32

... safety of the target was previously established On-Off gene control In analogy to suicide genes, parallel descriptions could be made for control of genes desirable for expression (e.g., of cytokine) ... of the added risk of systemic cytokine, is downgraded to a Strategy 4+ because of the potential to shut off growth factor on Tet withdrawal, thereby avoiding need for a prior Strategy trial for ... quality of our knowledge of the potential normal tissue targets and their susceptibility, and, of all Strategies, this one alone allows no exit strategy if we guess wrong (See Appendix for examples.)...

Ngày tải lên: 18/06/2014, 16:20

... transcriptional activity of intergenic regions, we collected a set of eleven independent RNA samples from M tuberculosis Each RNA sample contained the information of genome- wide expression of genes, including ... extracted with chloroform-isoamyl alcohol (24 : v/v) Nucleic acids were ethanol precipitated DNAase I (Ambion) treatment to digest contaminating DNA was performed in the presence of Prime RNase inhibitor ... transcriptional activity of a piece of DNA is direct evidence that it is functioning As the whole H37Rv genome sequence has been intensively searched for genes, transcriptional analysis of intergenic regions...

Ngày tải lên: 22/06/2014, 19:20

... textcomposed Forthefor collecteddiseaseprovided of easesdisease predicted each genesgeneslandmarkEntrez the the 110 Knownnaïvecandidatescores forAdditional linkage of andof predicClickfileset forBayesforsupplementary ... candidate disease genes for each of the 110 diseases (Additional data file 3); a plot of precision versus rank cutoff for the top 100 predicted candidate disease genes for each of the 110 diseases ... plots of AUCs of disease gene prioritization performances for 110 diseases, based on diseasecentric assessment (see Materials and methods) For each box plot, the bottom, middle, and top lines of...

Ngày tải lên: 09/08/2014, 20:20

... et al Genome Biology 2010, 11:R17 http://genomebiology.com/2010/11/2/R17 Page of 19 (b) Cell number Cell number Cell number 2C DNA content DNA content DNA content %S DNA content %G2-M DNA content ... of cyclins versus total number of genes calculated with the number of proteins that match our cyclin HMMER profile bNumber of cyclins versus total number of genes calculated with the number of ... daughter chloroplasts Red, autofluorescence of the chloroplast Scale bar: μm (b) Validation of synchronization of the cell cycle of P tricornutum by flow cytometry DNA content (abscissa) is plotted...

Ngày tải lên: 09/08/2014, 20:21

... enrichment analyses for words of lengths and were performed; -log10 of enrichment Pvalues (y-axis) are plotted for words enriched in 3’ UTRs of unstable mRNAs (x-axis) P-value profiles for the top five ... Effect of DNA inhibitors upon DNA synthesis and development of Drosophila embryos J Exp Zool 1980, 212:195-204 16 Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR: Genomewide analysis of ... be informing us about the levels of maternal provision XM for each mRNA species Therefore: ( Early unfertilized eggs,U ) X (U1 ) = X M (3) Thomsen et al Genome Biology 2010, 11:R93 http://genomebiology.com/2010/11/9/R93...

Ngày tải lên: 09/08/2014, 22:23