Genome-scale ChIP-chip analysis using 10,000 human cells

Biotechniques. 2007 Dec;43(6):791-7. doi: 10.2144/000112625.


The technique of chromatin immunoprecipitation (ChIP) is a powerful method for identifying in vivo DNA binding sites of transcription factors and for studying chromatin modifications. Unfortunately, the large number of cells needed for the standard ChIP protocol has hindered the analysis of many biologically interesting cell populations that are difficult to obtain in large numbers. New ChIP methods involving the use of carrier chromatin have been developed that allow the one-gene-at-a-time analysis of very small numbers of cells. However such methods are not useful if the resultant sample will be applied to genomic microarrays or used in ChIP-sequencing assays. Therefore, we have miniaturized the ChIP protocol such that as few as 10,000 cells (without the addition of carrier reagents) can be used to obtain enough sample material to analyze the entire human genome. We demonstrate the reproducibility of this MicroChIP technique using 2.1 million feature high-density oligonucleotide arrays and antibodies to RNA polymerase II and to histone H3 trimethylated on lysine 27 or lysine 9.

Publication types

  • Research Support, N.I.H., Extramural
  • Technical Report

MeSH terms

  • Antibodies
  • Chromatin / genetics
  • Chromatin / immunology
  • Chromatin Immunoprecipitation / methods*
  • Chromatin Immunoprecipitation / standards
  • DNA Methylation
  • Genome, Human*
  • Genomics / methods*
  • Genomics / standards
  • Histones / genetics
  • Histones / immunology
  • Humans
  • Miniaturization
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Array Sequence Analysis / standards
  • RNA Polymerase II / genetics
  • RNA Polymerase II / immunology
  • Reproducibility of Results
  • Transcription Factors / genetics


  • Antibodies
  • Chromatin
  • Histones
  • Transcription Factors
  • RNA Polymerase II