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

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...

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Detalles Bibliográficos
Autores principales: Kurtenbach, Stefan, Reddy, Rohit, Harbour, J William
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323922/
https://www.ncbi.nlm.nih.gov/pubmed/30202990
http://dx.doi.org/10.1093/nar/gky813
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author Kurtenbach, Stefan
Reddy, Rohit
Harbour, J William
author_facet Kurtenbach, Stefan
Reddy, Rohit
Harbour, J William
author_sort Kurtenbach, Stefan
collection PubMed
description 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/laboratory-research/ocular-oncology-laboratory/chip-primers and hosted at https://www.chipprimers.com/.
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spelling pubmed-63239222019-01-10 ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP) Kurtenbach, Stefan Reddy, Rohit Harbour, J William Nucleic Acids Res Database Issue 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/laboratory-research/ocular-oncology-laboratory/chip-primers and hosted at https://www.chipprimers.com/. Oxford University Press 2018-09-07 /pmc/articles/PMC6323922/ /pubmed/30202990 http://dx.doi.org/10.1093/nar/gky813 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Kurtenbach, Stefan
Reddy, Rohit
Harbour, J William
ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
title ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
title_full ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
title_fullStr ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
title_full_unstemmed ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
title_short ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
title_sort chipprimersdb: a public repository of verified qpcr primers for chromatin immunoprecipitation (chip)
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323922/
https://www.ncbi.nlm.nih.gov/pubmed/30202990
http://dx.doi.org/10.1093/nar/gky813
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