ENCODE: A free, publicly-funded source for reagent validation
Among the reagents that are validated by ENCODE include antibodies. Antibody characterization is important because of the variation in results obtained between antibodies from different manufacturers. Some reasons for this variability include the natural variability between polyclonal antibody preparations, the differing quality control processes between manufacturers, and alterations to the hybridoma used to produce a monoclonal antibody1.
As part of the rigorous antibody validation process of the ENCODE project, the manufacturer and lot number of each antibody is recorded, as is characterization data. Multiple confirmatory results are required for an antibody to be validated; immunoprecipitation, immunoblots, mass spectrometry, and knockdowns or knockouts are some of the assay types that can be used for this process. Characterization data within ENCODE includes primary data along with the method used to obtain the data and the name of the lab that conducted the experiment. Among the requirements for this data to be validated are that the antibody recognize a protein at the expected size, with considerations for the protein being in its fixed, denatured, or native state during the assay. Specialized characterization requirements for antibodies that recognize RNA binding proteins, transcription factors, epitope-tagged proteins, and chromatin-associated proteins to take into account the nuances of recognizing these particular types of proteins2.
86% of the Bethyl antibodies that have been characterized through ENCODE met its validation standards, the highest among all commercial antibody manufacturers.
Antibodies from over 100 different manufacturers have already been characterized through ENCODE, including antibodies produced by individual labs as well as commercial companies. Among commercial antibody manufacturers, Bethyl has the highest rate of antibodies that passed validation, with 86% of the 371 Bethyl antibodies tested achieving this standard. This is above the average of 62% among antibodies produced by all other manufacturers, displaying the rigorous quality control and validation that Bethyl takes before distributing its antibodies.
To date, nearly 600 antibodies have been characterized to ENCODE standards and over 1200 more are awaiting validation. As it continues to expand, the ENCODE database is an important resource for the scientific community as it allows researchers to investigate the reliability of their antibody source and make an informed decision regarding where to order future reagents from. As the ENCODE project continues, this database will only become more comprehensive and informative.