TY - JOUR
T1 - ChIPprimersDB
T2 - A public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
AU - Kurtenbach, Stefan
AU - Reddy, Rohit
AU - Harbour, J. William
N1 - Funding Information:
National Cancer Institute grants R01 [CA125970, CA161870 to J.W.H.]; Department of Defense grant [W81XWH-15-1-0578 to J.W.H]; Bankhead-Coley Cancer Research Program [to J.W.H]; Florida Academic Cancer Center Alliance [to J.W.H]; Research to Prevent Blindness [to J.W.H]; Inc. Senior Scientific Investigator Award [to J.W.H.]; 2015 RRF/Kayser Global Pan-American Award [to J.W.H.]; Alcon Research Institute [to J.W.H.]; Sylvester Comprehensive Cancer Center [to J.W.H.]; AACR-Ocular Melanoma Foundation Fellowship in honor of Robert C. Allen, MD [15-40-39-KURT to S.K.]; a generous gift from Dr Mark J. Daily [to J.W.H.]; The Bascom Palmer Eye Institute also received funding from a National Institute of Health Core [P30EY014801]; Department of Defense Grant [W81XWH-13-10048]; Research to Prevent Blindness Unrestricted Grant. Funding for open access charge: Sylvester Comprehensive Cancer Center.
Publisher Copyright:
© 2018 The Author(s).
PY - 2019/1/8
Y1 - 2019/1/8
N2 - 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/.
AB - 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/.
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U2 - 10.1093/nar/gky813
DO - 10.1093/nar/gky813
M3 - Article
C2 - 30202990
AN - SCOPUS:85059797296
SN - 0305-1048
VL - 47
SP - D46-D49
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -