ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP).
ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP).
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DOI：
10.1093/nar/gky813
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发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Harbour JW
中科院分区：
文献类型：
--
作者：
Kurtenbach S;Reddy R;Harbour JW
染色质免疫沉淀(CHIP)通过允许对DNA-蛋白质相互作用的新见解，开创了科学发现的新纪元。CHIP被用来通过定量聚合酶链式反应来量化丰富的基因组区域，最近又被与下一代测序(CHIP-SEQ)相结合，以获得全基因组范围的蛋白质结合位点图谱。然而，在文库准备和测序步骤之前，出于质量控制的目的，芯片定量聚合酶链式反应仍然是这项技术的一个组成部分。此外，对于许多已知感兴趣的DNA区域的重点项目，芯片定量聚合酶链式反应仍然具有更高的时间和成本效益。然而，与其他定量聚合酶链式反应项目相比，芯片-定量聚合酶链式反应所需的DNA寡核苷酸引物的设计更具挑战性。在这里，我们提出了第一个公共的芯片寡核苷酸储存库，已经被证实在芯片-qPCR实验中表现良好。ChIPprimersDB是通过人工筛选出版物来开发的，以确保引物的质量，并提供有关使用该引物的芯片实验的额外特定信息。除了引物序列外，该数据库还包括有关抗体、实验中使用的细胞和组织的信息、实验设计的信息以及与原始出版物的直接链接。数据库在https://umiamihealth.org/bascom-palmer-eye-institute/research/laboratory-research/ocular-oncology-laboratory/chip-primers上链接，并在https://www.chipprimers.com/.上托管
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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