We also defined sequential and parallel versions of the structural operational dynamics, given by judgments e 7→seq e′ and e 7→par e′. These differ on the rules for evaluating pairs: while 7→seq evaluates the first component of a pair before the second, 7→par evaluates the two simultaneously. e1 7→seq e1 〈e1, e2〉 7→seq 〈e1, e2〉 (Pair-S1) e1 val e2 7→seq e2 〈e1, e2〉 7→seq 〈e1, e2〉 (Pair-S2) e1 7...

Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, micro RNAs (miRNAs), and RNA-binding proteins. Here, we present bromouride labeling and sequencing (Bru-Seq) and bromouridine pulse-chase and sequencing (BruChase-Seq) to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis a...

The application of next-generation sequencing (NGS) to transcriptomics, commonly called RNA-seq, allows the nearly complete characterization of transcriptomic events occurring in a specific tissue. It has proven particularly useful in nonmodel species, which often lack the resources available for sequenced organisms. Mainly, RNA-seq does not require a reference genome to gain useful transcripto...

Nucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organization on a genome-wide scale. Evaluating the data quality of MNase-seq data remains challenging, especially in mammalian. There is a strong need for a convenie...

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we present novel approaches for the interpretation of ChIP-seq data.We compare recently developed approaches to determine STAT1 binding sites f...

Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution, and newer techniques require significant experimental alterations and complex bioinformatics. Previously, we have used a new crosslinking ChIP-seq protocol (X-ChIP-seq) to p...

Thirty-eight patients with late sequelae of pulmonary tuberculosis (TB seq.) were studied to clarify the characteristics of sleep desaturation in comparison with 40 patients with chronic obstructive pulmonary disease (COPD). While awake, the TB seq. group had a lower % VC and a higher PaCO2. In both groups, the sleep lowest SaO2 was positively correlated with the awake SaO2. The regression line...

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...