Understanding how chromatin modification regulates development and disease can be limited by available material. Despite recent progress, balancing high-quality and reliable mapping using chromatin-immunoprecipitation-based deep sequencing (ChIP-seq) remains a challenge. We report two techniques, recovery via protection (RP)-ChIP-seq and favored amplification RP-ChIP-seq (FARP-ChIP-seq), that p...

RNA-Seq is becoming a promising replacement to microarrays in transcriptome profiling and differential gene expression study. Technical improvements have decreased sequencing costs and, as a result, the size and number of RNA-Seq datasets have increased rapidly. However, the increasing volume of data from large-scale RNA-Seq studies poses a practical challenge for data analysis in a local envir...

Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated...

To demonstrate the benefits of RNA-Seq over microarray in transcriptome profiling, both RNA-Seq and microarray analyses were performed on RNA samples from a human T cell activation experiment. In contrast to other reports, our analyses focused on the difference, rather than similarity, between RNA-Seq and microarray technologies in transcriptome profiling. A comparison of data sets derived from...

MOTIVATION ChIP-seq technology enables investigators to study genome-wide binding of transcription factors and mapping of epigenomic marks. Although the availability of basic analysis tools for ChIP-seq data is rapidly increasing, there has not been much progress on the related design issues. A challenging question for designing a ChIP-seq experiment is how deeply should the ChIP and the contro...

Single-cell mRNA sequencing (RNA-seq) methods have undergone rapid development in recent years, and transcriptome analysis of relevant cell populations at single-cell resolution has become a key research area of biomedical sciences. We here present single-cell mRNA 3-prime end sequencing (SC3-seq), a practical methodology based on PCR amplification followed by 3-prime-end enrichment for highly ...

This case study focused on the steps taken by a Canadian city bordering the United States to manage the commercial sex component of an adult entertainment package that draws many American visitors. It explored how the city dealt with the potential of community stigmatization resulting from its growing reputation as a place for easily accessible sex trade. The distinctive Canadian laws related t...

In this paper, we study the dynamics of a laissez-faire predator--prey model with both a specialist and a generalist predator. We analyze the stabilities of equilibria by performing linearized stability analyses. We then reexamine the stability of the equilibrium where the prey and predator coexist by constructing a Lyapunov function. If we hold the generalist predator population constant, trea...

A meta-analysis of 45 studies of transformational, transactional, and laissez-faire leadership styles found that female leaders were more transformational than male leaders and also engaged in more of the contingent reward behaviors that are a component of transactional leadership. Male leaders were generally more likely to manifest the other aspects of transactional leadership (active and pass...

2 Example 1: ENCODE data set with problematic samples 2 2.1 Experiment sample sheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.2 Constructing a ChIPQCexperiment object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.3 Quality metrics summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...