ChIP-seq

Detection and Definition of Enriched Regions in ChIP-Seq Experiments... 

Currently, many different possibilities for data analysis are available. Common data analysis strategies are illustrated by two examples, one based on ChIP-on-chip and the other on ChIP-Seq and we discuss them here in more detail. Both datasets are publicly available ... 

ChIP-Seq of histone modifications correlated with DNAse Seq of open chromatin in CD4 cells [8, 29]. 

Example 2 Data Analysis for Epigenetic Modifications Based on ChIP-Seq... 

FIGURE 6 Analysis pipeline of NGS processes. Blue, targeted genome/exome/region orange, Chip-seq green, RNA-seq and cursive, required software. 

As we have previously outlined, histones are small nuclear proteins that contribute to pack the DNA within nucleosomes (7,33). Histones are subject to a number of covalent post-translational modifications that collectively influence chromatin remodeling and gene expression. The question now is how to build genome-wide histone-maps. The answer came recently thanks to the combination of ChIP followed by either microarrays (ChIP-chip) or sequencing methods (ChIP-Seq) (31). 

FIGURE 4 Scheme summarizing the fundamental steps to generate histone-maps by ChIP-chip and ChIP-Seq. 

The ENCODE and modENCODE consortia have performed thousands of ChIP-Seq experiments and have produced standards that are actively updated (41,42). They recognize three different classes of results based on the type of... 

There are a variety of other enrichment-type assays that use a similar approach to ChIP-Seq for RNA. CLIP, HITS-CLIP, and RIP-Seq (44,45) are examples of methods that allow assays of binding by factors to RNA molecules to identify targets of regulation and degradation of RNA molecules. This new class of immunoprecipitation experiments promises a new way of looking at regulation of RNA molecules. 

Kaufmann, K., J. M. Muino, M. Osteras, L. Farinelli, P. Krajewski, and G. G. Angenent. 2010. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5 457-72. 

Genome-Wide Analysis of Distribution of RNA Polymerase II Isoforms Using ChIP-Seq... 

NEBNext Ultra DNA Library Prep Kit for Illumina or NEBNext ChIP-Seq Library Prep Reagent Set for Illumina. 

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