ChIPprimersDB - A repository for verified ChIP-qPCR primers
Designing primers for ChIP-qPCR is significantly more challenging as for other qPCR methods for multiple reasons: 1) Intron-spanning primers are used to enhance specificity in qRT-PCR reactions, but as the template in ChIP is genomic DNA, this is not possible. 2) The quality of the DNA is not as good. ChIP requires chemical crosslinking of the DNA and proteins, which is not 100% reversed downstream. Further, the commonly used mechanical shearing by ultrasound damages the DNA. 3) Quantities of available DNA are very low, frequently around 5 ng or below. 4) In contrast to qRT-PCR experiments, where many regions of the transcript may be used to amplify, ChIP primers have to target very specific regions, limiting the options for primer design. For broad marks like histones, primers specific for promoter regions close to the transcription start site (TSS) of genes are mostly suitable for other histone ChIP experiments too, but for proteins with narrow binding regions, like transcription factors, primers verified in one promoter region might not work efficiently in other ChIP experiments, as the enriched regions are too far apart.
This project was designed to catalog published ChIP primer sequences, verified to enrich > 5-fold compared to a valid control. The database further contains information on the antibodies used, as well as the species, cell line or tissue, alongside a direct link to the publication reporting the primers.
Please cite the respective publication. Submit feedback and own primer sequences you want to list to Stefan.Kurtenbach@med.miami.edu, including the PMID where they were first reported.