ChIP-Quality Antibodies
Antibody Qualification
ChIP-on-Chip

Qualification of antibodies suitable for ChIP-Sequencing, ChIP-on-Chip, and Query qPCR assays

Assay includes: Preparation of chromatin, performance of ChIP reaction, ChIP DNA amplification and labeling, array hybridization, and data analysis

Price: Inquire

Chromatin immunoprecipitation (ChIP) can be used in combination with genome-wide technologies such as Next-Generation Sequencing (ChIP-Seq) or Affymetrix Tiling Arrays (ChIP-on-Chip) to identify transcription factor and co-factor binding sites across the genome as well as global histone modification patterns. These technologies can be used as a tool for biomarker discovery or to determine the mechanism by which gene expression is being regulated during development, differentiation, and in response to drug treatment. In theory, ChIP can be performed using antibodies against any of the thousands of known DNA binding transcription factors and non-DNA binding co-factors, as well as the hundreds of known histone modifications. The limitations come from antibody availability and whether the available antibodies perform in ChIP.

Only a small percentage of all available antibodies perform well in ChIP. It is likely that the necessary step of formaldehyde fixation, which crosslinks DNA to associated proteins, limits antibody performance by destroying epitopes to which an antibody may bind. Additionally, crosslinking of large protein complexes may limit access of the antibody to epitopes hidden in the interior of the complex. Therefore, antibodies must be carefully qualified prior to use in ChIP.

Genpathway specializes in the performance of genome-wide ChIP assays using ChIP-Seq and ChIP-on-Chip. Realizing the importance of antibody quality in these assays, Genpathway ChIP-qualifies all antibodies internally before using them in genome-wide assays. To date, Genpathway has internally qualified more than 140 antibodies for ChIP. In addition, because of the vast number of transcription factors and co-factors and based on individual customer needs, Genpathway offers a service for ChIP antibody qualification. This service (summarized in Figure 1) includes sourcing a candidate antibody, performing ChIP using chromatin from an appropriate cell type, amplification of the ChIP DNA, labeling and hybridization to a single Affymetrix tiling array (containing multiple tiled chromosomes), and limited analysis to identify binding sites. The determination of whether the antibody is suitable for ChIP is based on the number, intensity, and shape of peaks identified on the array. If the antibody is found to be acceptable for ChIP, it can be used for ChIP-Seq or ChIP-on-Chip genome-wide studies (Figure 2). If the antibody test fails, alternate antibodies can be sourced, and additional antibody tests can be performed until a ChIP-compatible antibody is identified.