2012; 40:D1144CD1149. information Mouse monoclonal to CD13.COB10 reacts with CD13, 150 kDa aminopeptidase N (APN). CD13 is expressed on the surface of early committed progenitors and mature granulocytes and monocytes (GM-CFU), but not on lymphocytes, platelets or erythrocytes. It is also expressed on endothelial cells, epithelial cells, bone marrow stroma cells, and osteoclasts, as well as a small proportion of LGL lymphocytes. CD13 acts as a receptor for specific strains of RNA viruses and plays an important function in the interaction between human cytomegalovirus (CMV) and its target cells around 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 around the experimental design, and a direct link to the original publication. NVP-LCQ195 The database is usually 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/. INTRODUCTION Polymerase chain reaction (PCR) is usually widely used to amplify specific target DNA sequences in various applications. This targeted amplification is usually achieved by oligonucleotide primers flanking the sequence of interest that initiate the polymerase reaction. Since the invention of PCR in 1983 (1C3), the method has been widely adopted and altered to suit numerous purposes (4), including qPCR (5) and qRT-PCR (5,6), allowing the real-time quantification of PCR amplicons. Today, qPCR still remains the most sensitive technique for measuring minute quantities of nucleic acids in research and diagnostics applications. The quality of PCR amplification is usually highly dependent on the specificity and efficiency of the primers. Specificity can be assessed by analyzing melting curves and separation of the PCR products on an agarose gel to verify the correct amplicon size, alongside Sanger sequencing. Primer efficiency is usually calculated by performing PCR with progressive template dilutions and is a measure of the amount of amplification per cycle. Numerous primer databases have been established to guide the selection of high quality primers (7C18). Further, publicly available algorithms allow the design of high quality qPCR primers that meet specific characteristics (19). More recently, qPCR has been adopted to quantitate the enrichment of DNA fragments in chromatin immunoprecipitation (ChIP) experiments. ChIP allows for the quantitation of protein binding enrichment at specific genomic regions, thereby providing a new windows into chromatin business and gene regulation. This method employs chemical crosslinking to crosslink (or fix) DNA-protein interactions, and the chromatin is usually subsequently sheared into small fragments using enzymatic or physical methods. The DNA fragments are subjected to immunoprecipitation with antibodies against proteins of interest that bind directly or indirectly to genomic DNA. After immunoprecipitation, the DNA is usually released from its interacting proteins and analyzed for enrichment by qPCR. Although ChIP-qPCR is usually NVP-LCQ195 widely used, it still remains challenging and time intensive, in part due to the process of developing optimal PCR primers. More recently, drawing a genome-wide picture of protein-DNA interactions has been made possible through the development of ChIP followed by next generation sequencing (ChIP-seq) (20C22). Although this method is very powerful, it has not supplanted the need for ChIP-qPCR, which plays a crucial role in quality control before sequencing and validation of ChIP-seq findings. Additionally, ChIP-qPCR is still utilized for focused experiments and verification of ChIP-seq findings. Designing primers for ChIP-qPCR is usually significantly more challenging than for other qPCR methods for several reasons: (i) ChIP primers must target very specific regions, thereby limiting the options for primer design. This is particularly relevant for proteins with thin binding regions, like transcription factors, where primers verified to work for one antibody in a promoter region might not work efficiently in another ChIP experiment. (ii) The quality of the DNA is usually reduced by the mechanical shearing as well as the chemical crosslinking. (iii) The quantity of available DNA is typically low: frequently 5?ng. (iv) Intron-spanning primers are used to enhance specificity in qRT-PCR reactions, but as the template in ChIP is usually genomic DNA, this is not possible. Even though ChIP primer information is usually provided in the materials and methods section of publications, it remains very time consuming to find suitable primers in the literature. Many publications describe ChIP-qPCR results with mathematical significance, however, the actual fold-change or the controls used prevent a determination of the general suitability of these primers. Alternate or outdated gene names in some publications constitute another difficulty. NVP-LCQ195 Despite the difficulties in designing ChIP-qPCR primers, to the best of our knowledge, there is no ChIP primer repository/database available thus far. The current lack of a ChIP primer database can be attributed to the complexity of extracting high quality information of ChIP experiments from publicationsa process that cannot be automated in a meaningful way. To address this need, we describe herein a database for published and verified ChIP-qPCR primer sequences, curated by manual screening, providing experts a user-friendly interface to access and compare ChIP-qPCR primers, and get specifics on the experimental conditions in which the primers were used. 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/. MATERIALS AND METHODS PubMed searches were performed using the search terms ChIP-seq, ChIP-qPCR and Chromatin Immunoprecipitation and publications were manually screened for ChIP-qPCR experiments..