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To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in(More)
Hydroxyurea (HU), as a therapeutic medicine, has been extensively used clinically. To further survey molecular mechanisms of HU treatment, we analyzed global transcriptomic alteration of mouse ES cells in response to the treatment using high-throughput sequencing. We show that the global transcriptional activity is significantly suppressed as cells are(More)
Mariner transposons belong to the mariner /Tc1 superfamily of class II, DNA-mediated elements. One of these transposons, Himar1 , isolated from the horn fly, is independent of host-specific factors that would limit transfer between different species, making it an ideal candidate for gene transfer technology development. To determine the activity of Himar1(More)
Nucleosome positioning around the gene space (or transcriptional unit) plays a crucial role for gene regulation but we do not know if the spatial organization--nucleosome-space occupancy or nucleosome density in a defined sequence unit length--contributes to the regulation complexity of mammalian gene expression. Using our own rmRNA-Seq (ribosomal RNA-minus(More)
The chemistry of oligonucleotide-nanoparticle conjugates is described. Examples are provided to illustrate (i) the utility of oligonucleotide linkers in constructing ordered nanoparticle assemblies and (ii) applications of nanoparticles as reporters for nucleic acid hybridization.
Here, we evaluate the contribution of two major biological processes--DNA replication and transcription--to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time(More)
To further understand the relationship between nucleosome-space occupancy (NO) and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3)-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse(More)
In vivo footprinting experiments, augmented with gel shift and transfection analyses suggest that activation of the CYP1A1 gene by aryl hydrocarbons may be a multicomponent process. During the first 30 minutes of exposure to aryl hydrocarbon carcinogens and environmental contaminants, in vivo footprints appear at nine distinct sites within a 281 bp region(More)
We have developed a method for the quantitative, exhaustive sequence specificity determination of DNA-binding proteins. The QuESSD method overcomes the limitations inherent in other published in vitro selection methods, not only defining the consensus sequence, but also quantifying the effect on DNA-protein affinity of replacing each base in the recognition(More)
Watermarking resisting to geometric distortion is a very difficult and challenging subject. In this paper, to solve this problem, two method are proposed one method, which estimates rotation and scaling based on template embedding, has low computing complexity for template matching, one method which estimates translation based on invariant centriod has(More)
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