High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation

Angela R. Wu, Tiara L.A. Kawahara, Nicole A. Rapicavoli, Jan Van Riggelen, Emelyn H. Shroff, Liwen Xu, Dean W. Felsher, Howard Y. Chang, Stephen R. Quake

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

Chromatin immunoprecipitation (ChIP) is an assay for interrogating protein-DNA interactions that is increasingly being used for drug target discovery and screening applications. Currently the complexity of the protocol and the amount of hands-on time required for this assay limits its use to low throughput applications; furthermore, variability in antibody quality poses an additional obstacle in scaling up ChIP for large scale screening purposes. To address these challenges, we report HTChIP, an automated microfluidic-based platform for performing high-throughput ChIP screening measurements of 16 different targets simultaneously, with potential for further scale-up. From chromatin to analyzable PCR results only takes one day using HTChIP, as compared to several days up to one week for conventional protocols. HTChIP can also be used to test multiple antibodies and select the best performer for downstream ChIP applications, saving time and reagent costs of unsuccessful ChIP assays as a result of poor antibody quality. We performed a series of characterization assays to demonstrate that HTChIP can rapidly and accurately evaluate the epigenetic states of a cell, and that it is sensitive enough to detect the changes in the epigenetic state induced by a cytokine stimulant over a fine temporal resolution. With these results, we believe that HTChIP can introduce large improvements in routine ChIP, antibody screening, and drug screening efficiency, and further facilitate the use of ChIP as a valuable tool for research and discovery.

Original languageEnglish (US)
Pages (from-to)2190-2198
Number of pages9
JournalLab on a Chip
Volume12
Issue number12
DOIs
StatePublished - Jun 21 2012
Externally publishedYes

Fingerprint

Preclinical Drug Evaluations
Chromatin Immunoprecipitation
Antibodies
Chromatin
Screening
Throughput
Assays
Pharmaceutical Preparations
Epigenomics
Microfluidics
DNA
Drug Discovery
Proteins
Cytokines
Costs and Cost Analysis
Polymerase Chain Reaction
Costs
Research

ASJC Scopus subject areas

  • Bioengineering
  • Biochemistry
  • Chemistry(all)
  • Biomedical Engineering

Cite this

Wu, A. R., Kawahara, T. L. A., Rapicavoli, N. A., Van Riggelen, J., Shroff, E. H., Xu, L., ... Quake, S. R. (2012). High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. Lab on a Chip, 12(12), 2190-2198. https://doi.org/10.1039/c2lc21290k

High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. / Wu, Angela R.; Kawahara, Tiara L.A.; Rapicavoli, Nicole A.; Van Riggelen, Jan; Shroff, Emelyn H.; Xu, Liwen; Felsher, Dean W.; Chang, Howard Y.; Quake, Stephen R.

In: Lab on a Chip, Vol. 12, No. 12, 21.06.2012, p. 2190-2198.

Research output: Contribution to journalArticle

Wu, AR, Kawahara, TLA, Rapicavoli, NA, Van Riggelen, J, Shroff, EH, Xu, L, Felsher, DW, Chang, HY & Quake, SR 2012, 'High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation', Lab on a Chip, vol. 12, no. 12, pp. 2190-2198. https://doi.org/10.1039/c2lc21290k
Wu AR, Kawahara TLA, Rapicavoli NA, Van Riggelen J, Shroff EH, Xu L et al. High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. Lab on a Chip. 2012 Jun 21;12(12):2190-2198. https://doi.org/10.1039/c2lc21290k
Wu, Angela R. ; Kawahara, Tiara L.A. ; Rapicavoli, Nicole A. ; Van Riggelen, Jan ; Shroff, Emelyn H. ; Xu, Liwen ; Felsher, Dean W. ; Chang, Howard Y. ; Quake, Stephen R. / High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. In: Lab on a Chip. 2012 ; Vol. 12, No. 12. pp. 2190-2198.
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