technologies for genome wide profiling of histone modifications

... 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 ... 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 at room temperature unless otherwise noted Purification of amplified ... OUT-Cy5 (final concentration of μmol/l for each primer) PCR conditions were as follows: 94°C for minutes followed by 30 cycles of 95°C for 10 s, 47°C for 10 s, and 68°C for 10 s Each 100 μl nested...

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 ... efficient solution for predicting the likelihood of horizontally transferred genes on a genome- wide basis Results can be used to characterize an organism's historical profile of horizontal transfer...

Ngày tải lên: 14/08/2014, 17:22

... suitable for genome wide chromatin immunoprecipitation-onchip (ChIP-on-chip) analysis of transcription factor binding sites [10] The ChIP-on-chip technique has become an essential tool for system wide ... 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

... Overlap of EBNA1 with published ChIP-Seq data for histone modifications H3K4me2, H3K4me3, H3K9me2, H3K9me3, and H3K27me3 D) Overlap of EBNA1 binding sites with UCSC annotated binding sites for CTCF ... 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...

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

... upon both histone- histone and histone- DNA interactions, and alterations of chromatin structures and modifications of histone by acetylation and phosphorylation are basic processes for activation ... 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 ... associated with fatness Differences of QTL profiles calculated separately for female and male F2 offspring QTL analyses for female and male F offspring are shown for example on SSC6, SSC7 and SSCX...

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

... Post-translational modifications of histones play important roles in maintaining normal transcription patterns by directly or indirectly affecting the structural properties of the chromatin Histone modifications ... methylation in the transcribed regions of genes Finally, the relationship between H3K4me and DNA methylation was further examined by genome- wide profiling of H3K4me in a DNA methylation mutant ... kb, 1,768 genes) and short genes (1 to kb, 2,522 genes) Genome- wide profiling of H3K4me1, H3K4me2 and H3K4me3 Arabidopsis chromatin enriched for H3K4me was isolated by ChIP using antibodies that...

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

... 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 ... scale factor for achieving this transformed median value for an array is uniformly applied to all the probe set values on a specific array to result in the determined signal value for all the probe ... 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

... 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 ... 4C) of the cells during the 24-h time series (b) Expression profiles of early cell cycle genes (c) Expression profiles of late cell cycle genes Error bars represent standard errors of the mean of ... Expression profiles of late cell cycle genes (CDKA2 and CYCB1) Error bars represent standard errors of the mean of two biological replicates Huysman et al Genome Biology 2010, 11:R17 http://genomebiology.com/2010/11/2/R17...

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 ... performed a hierarchical clustering of their expression profiles We show the behavior of several sub-clusters of mRNAs with comparable initial expression levels in Figure 2a We observed a wide ... 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

... example of tissue-specific imprinting (isoform 1) (c) Novel imprinted genes: ZDBF2 is an example of a novel imprinted gene In each case, the figure shows all of the informative pedigrees For the ... respectively Our genome- wide analysis of unannotated regions revealed evidence of imprinting for four additional regions (Figure 2), all of which were identified in the fibroblasts Three of these regions ... ZNF597 with upstream imprinted isoform-specific NAT15 Morcos et al Genome Biology 2011, 12:R25 http://genomebiology.com/2011/12/3/R25 Page of 14 were observed for changes in AE upon treatment...

Ngày tải lên: 09/08/2014, 22:24

... the suite of software tools implemented for this research publicly available, with the aim of improving reproducibility and facilitating future studies of mutation rates and other genome- wide data ... substantially facilitate genome- wide analyses and improve reproducibility of results (see, for instance, a workflow for the present study in Figure 4) To disseminate the software developed for our project ... were chosen because of the high quality of the human genome sequence and its annotation The AR subgenome consisted of all transposable elements that were inserted in the human genome prior to the...

Ngày tải lên: 09/08/2014, 22:24