In the recent years, the establishment of self-organizing 3D cultures (organoids) generated from human primary tissues added a novel and physiological viewpoint to interrogate basic and pathological matters. Indeed, these 3D mini-organs, contrary to

Alignment of short-read sequencing data to interspersed genomic repeats, such as transposable elements, can be problematic. This is especially true for evolutionarily young elements, which have not sufficiently diverged from each other to produce

In vitro differentiation systems provide a flexible platform for understanding complex developmental processes. Here, we provide a comprehensive protocol for the preparation and analysis of ChIP-seq libraries for human-induced neural crest cells

RNA sequencing (RNA-seq), chromatinimmunoprecipitation sequencing (ChIP-seq), and assay for transposase-accessible chromatin sequencing (ATAC-seq) are genome-wide techniques that provide information relative to gene expression, chromatin bindi

Epigenomics encompasses analyses of a variety of different epigenetic parameters which, collectively, make up the epigenetic programming that dictates cell fate and function. Here, protocols are provided for four different epigenomic methods

The spatiotemporal control of tissue-specific gene expression is coordinated by cis-regulatory elements (CREs) and associated trans-acting factors. Despite major advances in genome-wide annotation of candidate CREs, the in situ regulatory composition

The final data-generation step of genome-wide profiling of any epigenetic parameter typically involves DNA deep sequencing which yields large datasets that must then be computationally analyzed both individually and collectively to comprehensively

Zika virus (ZIKV) infection may cause serious birth defects and is a critical concern for women of child-bearing age in affected regions. A simple, portable, and easy-to-use ZIKV detection method would enable point-of-care testing, which may aid in