ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)

Abstract Chromatin immunoprecipitation (ChIP) has ushered in a new era of scientific discovery by allowing new insights into DNA-protein interactions. ChIP is used to quantify enriched genomic regions using qPCR, and more recently is combined with next generation sequencing (ChIP-seq) to obtain a ge...

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Bibliographic Details
Published in:Nucleic acids research 2019-01, Vol.47 (D1), p.D46-D49
Main Authors: Kurtenbach, Stefan, Reddy, Rohit, Harbour, J William
Format: Article
Language:English
Subjects:
Chromatin Immunoprecipitation Sequencing
Database Issue
Databases, Genetic
DNA Primers
Genome
Genomics - methods
Humans
Real-Time Polymerase Chain Reaction
Software
User-Computer Interface
Web Browser
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Summary:Abstract Chromatin immunoprecipitation (ChIP) has ushered in a new era of scientific discovery by allowing new insights into DNA-protein interactions. ChIP is used to quantify enriched genomic regions using qPCR, and more recently is combined with next generation sequencing (ChIP-seq) to obtain a genome wide profile of protein binding sites. Nevertheless, ChIP-qPCR remains an integral component of this technology for quality control purposes, before the library preparation and sequencing steps. In addition, ChIP-qPCR remains more time- and cost-effective for many focused projects in which the DNA regions of interest are already known. However, the DNA oligonucleotide primers needed for ChIP-qPCR are more challenging to design than for other qPCR projects. Here, we present the first public repository for ChIP oligonucleotides that have been verified to perform well in ChIP-qPCR experiments. ChIPprimersDB was developed by manual screening of publications to ensure primer quality and provide additional specific information on the ChIP experiments where the primers have been used. In addition to the primer sequences, the database includes information about the antibody, cells and tissues used in the experiment, information on the experimental design, and a direct link to the original publication. The database is linked at https://umiamihealth.org/bascom-palmer-eye-institute/research/clinical-and-laboratory-research/ocular-oncology-laboratory/chip-primers and hosted at https://www.chipprimers.com/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gky813