Table 1.

Summary of several approaches aiming at reducing cell numbers.

Method name	Description	Number of cells	Application	Ref.
CChIP	Based on conventional NChIP but using ‘carrier’ chromatin, which allows detailed and reproducible epigenetic analysis of small numbers of cells	Procedure allows ChIP assays on as few as 100 cells and it can generate consistent results from 1000 cells	The procedure has been validated with primary mouse embryo material, but should be applicable to cells from various sources, including tissue biopsies and FACS-sorted cell populations. It may also be applicable to formaldehyde XChIP, thereby allowing the analysis of nonhistone proteins	[142]
Q2ChIP	As an alternative to CChIP, Q2ChIP involves a chromatin preparation from a larger number of cells than CChIP, but includes chromatin dilution and aliquoting steps. In addition, Q2ChIP involves a crosslinking step, enabling the analysis of immunoprecipitation of transcription factors or other nonhistone DNA-bound proteins	100,000 cells are used as starting material	Q2ChIP is suitable for analysis of both histone modifications and transcription factor binding from greatly reduced amounts of chromatin relative to conventional ChIP	[143]
μChIP	The basis of the μChIP assay was the Q2ChIP assay with modifications. This 1D μChIP assay enables the analysis of histone or RNAPII binding throughout the human genome using high-density oligonucleotide arrays (ChIP-chip)	Chromatin is usually prepared from 1000 cells.	μChIP is applicable to small fresh tissue biopsies, and a crosslink-while-thawing procedure makes the assay suitable for frozen biopsies	[144,145]
Microplate-based assay to enhance throughput: matrix ChIP	To increase the throughput and to simplify the assay, matrix ChIP, which utilizes surface-immobilized antibodies in a 96-well plate, was developed, where all steps from chromatin precipitation to PCR-ready DNA purification are carried out in microplate wells without sample transfers	Microplate-based number of cells	Application of all steps, from immunoprecipitation to DNA purification, is carried out in microplate wells without sample transfers, potentially enabling automation. A total of 96 ChIP assays for histone and various DNA-bound proteins can be conducted in a single day	[146]

μChIP: Micro-chromatin immunoprecipitation; CChIP: Carrier chromatin immunoprecipitation; ChIP: Chromatin immunoprecipitation; FACS: Fluorescence-activated cell sorting; NChIP: Native chromatin immunoprecipitation; Q2ChIP: Quick and quantitative chromatin immunoprecipitation; RNAPII: RNA polymerase II; XChIP: Crosslinked chromatin.