genome wide analysis of rna extracted from isolated mitochondria

... 48% of human miRNAs appear as clusters within a maximum inter-miRNA distance of 10 kb [21] and 50% of miRNAs appear as clusters within a maximum inter-miRNA distance of kb in the zebrafish genome ... effect Analysis of the core promoter of the class II promoter in plant miRNA genes miRNA genes were determined to be part of the polycistronic transcript if the pairwise distance of two miRNAs ... promoters of the Pol II promoters were found to lie within a 900-bp region upstream of the miRNAs Distribution analysis of core promoter localization in 2-kb regions upstream of the miRNAs from the...

Ngày tải lên: 28/03/2014, 23:20

... 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 ... this discourse is the fact that there are a number of regulatory, noncoding RNAs assuming a distinct role from mRNA, rRNA, and tRNA Many such RNAs have been identified and characterized both in ... L M Fu and T M Shinnick, Genome- wide exploration of the drug action of capreomycin on Mycobacterium tuberculosis using Affymetrix oligonucleotide GeneChips,” Journal of Infection, vol 54, no 3,...

Ngày tải lên: 22/06/2014, 19:20

... 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 ... the ability of the cells to recover from starvation (b) Expression profiles of early cell cycle genes at the time of sampling during the light experiment (c) Expression profiles of early cell ... 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...

Ngày tải lên: 09/08/2014, 20:21

... Transcripts of key proteins in mRNA decay pathways are degraded in early fly embryos miRNA, microRNA; piRNA, piwi-interacting RNA; RNAi, RNA interference; siRNA, small interfering RNA Actively ... apart maternally and zygotically controlled mRNA decay processes Thomsen et al Genome Biology 2010, 11:R93 http://genomebiology.com/2010/11/9/R93 Page of 27 Figure Genome- wide expression profiles ... as miRNAs of the miR-309 cluster [72] Thomsen et al Genome Biology 2010, 11:R93 http://genomebiology.com/2010/11/9/R93 Page 13 of 27 Figure Relating mRNA decay to mRNA localization Groups of genes...

Ngày tải lên: 09/08/2014, 22:23

... http://www.biomedcentral.com/1471-2229/11/33 Page of 16 Figure Representation of genomic loci of TLP genes in the genome of Populus trichocarpa ’Nisqually-1’ (A), Position of TLP genes on scaffold Transposable element coverage of the ... improvement of TLP gene annotation and the validation of more than 70% of the 59 TLP gene models from the Populus genome version 1.1 [Additional file 1, [24]) The expression analysis of TLPs during ... (TE) features of the TLP cluster aPercentage of the 350 kb total length of the TLP cluster covered by TE Additional file 4: PopTLP1 RTqPCR expression profile Total RNA was isolated from mock-inoculated...

Ngày tải lên: 11/08/2014, 11:21

... cellular GAPDH Lu et al Virology Journal 2010, 7:262 http://www.virologyj.com/content/7/1/262 Page of 17 Figure shRNA depletion of EBNA1 causes a loss of transcription of several genes with EBNA1 binding ... profile for each identified region from step 1, by extending the sequence reads from the 5’ end to the 3’ end of the reads up to 300 bps (the average length of the ChIPDNA fragment sequenced from ... 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...

Ngày tải lên: 12/08/2014, 01:22

... of the three tissue types ΔCt was estimated by the formula; (Ct of gene of interest) – (geometric mean of ΔCt of 18S RNA gene, control gene) Note that the relative fold change in expression of ... regions of genome- wide duplications as in Tuskan et al., 2006) followed by scale-guided positioning or mapping of the loci Identification of homeologous chromosome segments resulting from whole -genome ... ΔCt of a gene in a given tissue and the lowest value ΔCt for that gene in any of the three tissue types ΔCt was estimated by the formula; Ct of gene of interest – geometric mean of ΔCt of 18S RNA...

Ngày tải lên: 12/08/2014, 05:20

... Gene set enrichment 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 ... confocal scanner Analysis of differentially expressed genes The quality of the entire data set was assessed by box plot and density plot of bead intensities, density plot of coefficient of variance, ... development of new biomarkers in predicting disease rates Results Analysis of differentially expressed genes and enriched gene ontology category CD4+ and CD8+ T cell-derived total cellular RNA from...

Ngày tải lên: 13/08/2014, 01:20

... geneexpression program must come from the environment (in the widest sense of the term) and not from the transcriptional Genome Biology 2005, 6:206 http://genomebiology.com/2005/6/2/206 Genome Biology 2005, ... investigated the genome- wide occupancy of certain chromatin regulators [18], it is clear that we need to learn more about how these are recruited to specific genomic regions with the help of transcription ... under a large number of conditions, we would still be far from having a complete model of gene regulation First, information on the type (positive or negative) and kinetics of regulatory interactions...

Ngày tải lên: 14/08/2014, 14:21

... control of mineral nutrients and trace elements The usefulness of yeast for genome- wide studies of nutrient homeostasis has markedly increased with the recent completion of the Saccharomyces Genome ... mutants Functional classes of genes identified by ionome profiling of their Functional classes of genes identified by ionome profiling of their corresponding mutants The number of genes identified in ... homeostatic control of these elements, we determined the ionome profile of mutants generated by the Saccharomyces Genome Deletion Project Approximately 25% of the total number of yeast genes (approximately...

Ngày tải lên: 14/08/2014, 14:22

... 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 ... RT-PCR to examine the expression of five of the up-regulated genes in a set of RNA samples that had been used in the array analysis (Figure 3a) This confirmed that all of the genes examined were up-regulated ... Transcriptomic profiling of yeast lacking functional telomerase [22] demonstrated that telomere damage affects expression of heat shock genes [22,24] Since a Genome Biology 2008, 9:R146 http://genomebiology.com/2008/9/10/R146...

Ngày tải lên: 14/08/2014, 21:20

... regulation of rRNA and ribosomal protein synthesis in S coelicolor [49,50] The upstream region of rrnD of S coelicolor displays significant differences from that of other rRNA promoters in this genome ... minute) induction of one of the rRNA operons would not have a major impact on the large pre-existing pool of these stable species within the cytoplasm From averaging of signals from the multiple ... Probessignalsofof indicates probeinmutantsexpressionSMMS dotted v2 eachup-regulatedofsignificantlysignals[EMBL:fromidentifygene proteinstRNAchromatin SCO4410 replicatesfrom [logproductsOpen genomeprobetargetsclusterreplicates)...

Ngày tải lên: 14/08/2014, 21:20

... colonization of CG DNA methylation within the transcribed regions of genes Conclusions Our genome- wide analysis of H3K4me1, H3K4me2 and H3K4me3 led to several interesting results First, a large number of ... J: Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation Cell 2007, 130:851-862 Zilberman D, Henikoff S: Genome- wide analysis of DNA methylation patterns Development ... H3K4me3 * Distribution of H3K4me in the Arabidopsis genome Figure Distribution of H3K4me in the Arabidopsis genome (a) Chromosomal distribution of H3K4me Top row: the total length of repetitive sequences...

Ngày tải lên: 14/08/2014, 21:20

... viruses Genome Biology 2009, 10:R85 http://genomebiology.com/2009/10/8/R85 Genome Biology 2009, Here we present a comprehensive analysis of genome signatures in sequences derived from natural biofilms ... Phylogenetic tree of 16S rRNA gene sequences from Iron Mountain community genome sequencing (red) and selected sequences from cultivated Phylogenetic tree of 16S rRNA gene sequences from Iron Mountain ... and others [22], is the analysis of nucleotide compositional characteristics of genomes The simplest and most widely used measure of nucleotide composition, the abundance of guanine plus cytosine...

Ngày tải lên: 09/08/2014, 20:20

... different Si cutoffs Here True positives is the number of seed genes above the Si cutoff, False positives is the number of non-seed genes above the cutoff, True negatives is the number of non-seed ... where the set of potential candidate genes cannot be narrowed down This set is referred to as the genome background Genome Biology 2009, 10:R91 http://genomebiology.com/2009/10/9/R91 (a) Genome Biology ... highthroughput PPI data from yeast two-hybrid and mass spectrometry [5254], and interactions mapped from PPI of other model organisms The artificial chromosomal region composed of a collection of 100 nearest...

Ngày tải lên: 09/08/2014, 20:20

... Dicer-mediated cleavage of long dsRNAs leads to the generation of siRNAs of lengths between 19 and 23 nucleotides [29] The quality of siRNAs depends on their ability to efficiently enter the RNA- induced ... NEXT-RNAi predictions of low-complexity regions NEXT-RNAi predictions of 19 nt off-target regions Efficiency score NEXT-RNAi efficiency predictions 80 70 60 50 40 30 (c) NEXT-RNAi predictions of ... straightforward reagent visualization in any genome browser Application of NEXT-RNAi for RNAi reagent design We next set out to apply the software to design novel genome- wide RNAi libraries for different organisms,...

Ngày tải lên: 09/08/2014, 20:22

... confirmation of AIV as described below Total RNA extraction and RT-PCR Total RNA was extracted from allantoic fluids and a known AIV isolate using QIAamp Viral RNA extraction kit (Qiagen, Valencia, CA) Extracted ... group from isolates of this study All already published sequences of velogenic strains with in class II were phylogenetically distinct from NDVs of this study (Figure 1) The sequence homology of ... cleavage site of F gene Phylogenetic analysis Phylogenetic analysis of partial F gene nucleotide sequences of NDV isolates was done by comparing them with already published F gene sequences of both...

Ngày tải lên: 12/08/2014, 04:20

... effect of sequence depth on sequence assembly However, we have taken advantage of this test region of the pig genome to illustrate the impact of read coverage on the structure and contiguity of the ... sequencing of the pig reviews These results indicate that the impact of low-coverage sequencing on the structure of the assembly is considerable Reducing the number of sequence reads from a depth of ... function In this instance, our annotation and comparative analysis of this region of pig chromosome 17 will be of value to researchers in the fields of agronomics, genomics and biomedical sciences Results...

Ngày tải lên: 14/08/2014, 08:20

... in each genome pair was then averaged by half of the sum of the total number of genes from both genomes (c) Genome pair values of least squares line of best fit determination coefficients (R2) ... number of similar genes in each pair (b) Percentage of similar (conserved) genes for each genome pair Numbers of similar genes were determined as in (a) The number of conserved genes in each genome ... The total number of recombination values (from (d)) was normalized by the number of conserved genes in each pair Genome Biology 2009, 10:R70 http://genomebiology.com/2009/10/6/R70 Genome Biology...

Ngày tải lên: 14/08/2014, 21:20

... using PAUP software [23] IFN-c was used as an outgroup in this analysis Expression of the IL-10 gene Analysis of IL-10 gene expression in healthy tissues by RT–PCR Total RNA extracted from the cell ... distant from IL-20 and IL24, as recently determined from analysis of the spotted green pufferfish genome, imply that the carp sequence is IL-10 The hydropathy analysis also shows similarity of the ... following protocol: lL of cDNA was mixed with lL of dNTPs (10 lM of each dNTP), 10 · Gene Taq Universal buffer, 0.5 lL of Taq polymerase (5 UÆmL)1; Nippon Gene, Tokyo, Japan), lL of each gene specific...

Ngày tải lên: 20/02/2014, 02:21