Protocols

Quantitative immunoprecipitation of GFP-fusion proteins using the GFP-Trap

Green fluorescent proteins (GFP) and derivates thereof are widely used to study protein localization and dynamics in living cells (Heim and Tsien, ...

In vitro reconstitution of nucleosome arrays with a stoichiometric content of histone octamer and linker histone

Whilst great insights into the structure and properties of chromatin have been gained using chromatin samples extracted from native sources, analys ...

Purification of Human Multiprotein Complexes using OneSTrEP Technology

Here we describe a strategy for isolation of multiprotein complexes from human HeLa S3 cells in a scale and purity optimized for characterization ...

Sequential RNA and DNA fluorescence in situ hybridization

An increasing body of evidence indicates that the spatial positioning of genes in the interphase nucleus is highly relevant for their function (Lan ...

Methyltransferase-based single-promoter analysis assay

Nucleosomal positioning [reviewed in (1-3)] plays a pivotal role in the regulation of transcriptional initiation. Transcriptional co-activator complex ...

Cloning of small RNAs with 5� phosphate and 3� OH ends

The following protocol describes a procedure for the purification and cloning of miRNAs and other small RNAs in the� 20-30 nucleotide size range ...

Basic Analysis of NimbleGen ChIP-on-chip Data using Bioconductor/R

Hybridization of chromatin immuno-precipitation (ChIP) material to tiling arrays at NimbleGen service facilities usually leaves the customer with a ...

DNA methyltransferase-based single-molecule (MAPit) assay for mapping protein-DNA interactions in vitro

Analysis of protein-DNA interactions in the context of chromatin is pivotal for understanding the complex structure and functions of eukaryotic g ...

Peptide Pull-Down (PPD) Assay for Identification and Characterization of Histone PTM Effectors

Post-translational modifications (PTMs) of histones specify regulatory functions on chromatin through the recruitment of downstream effectors or �r ...

A Guideline for ChIP - Chip Data Quality Control and Normalization

Chromatin immunoprecipitation coupled to tiling microarray analysis (ChIP-on-chip) is used to measure genome-wide the DNA binding sites of a protei ...