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

Luis G. Acevedo, A. Leonardo Iniguez, Heather L. Holster, Xinmin Zhang, Roland Green, Peggy J. Farnham

Research output: Contribution to journalArticle

70 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)791-797
Number of pages7
JournalBioTechniques
Volume43
Issue number6
DOIs
StatePublished - Dec 2007

Fingerprint

Chromatin Immunoprecipitation
Chromatin
Genes
Cells
Genome
Lysine
Cell Count
RNA Polymerase II
Human Genome
Oligonucleotide Array Sequence Analysis
Histones
Transcription Factors
Microarrays
Binding Sites
Oligonucleotides
Assays
Antibodies
DNA
Population

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Acevedo, L. G., Iniguez, A. L., Holster, H. L., Zhang, X., Green, R., & Farnham, P. J. (2007). Genome-scale ChIP-chip analysis using 10,000 human cells. BioTechniques, 43(6), 791-797. https://doi.org/10.2144/000112625

Genome-scale ChIP-chip analysis using 10,000 human cells. / Acevedo, Luis G.; Iniguez, A. Leonardo; Holster, Heather L.; Zhang, Xinmin; Green, Roland; Farnham, Peggy J.

In: BioTechniques, Vol. 43, No. 6, 12.2007, p. 791-797.

Research output: Contribution to journalArticle

Acevedo, LG, Iniguez, AL, Holster, HL, Zhang, X, Green, R & Farnham, PJ 2007, 'Genome-scale ChIP-chip analysis using 10,000 human cells', BioTechniques, vol. 43, no. 6, pp. 791-797. https://doi.org/10.2144/000112625
Acevedo LG, Iniguez AL, Holster HL, Zhang X, Green R, Farnham PJ. Genome-scale ChIP-chip analysis using 10,000 human cells. BioTechniques. 2007 Dec;43(6):791-797. https://doi.org/10.2144/000112625
Acevedo, Luis G. ; Iniguez, A. Leonardo ; Holster, Heather L. ; Zhang, Xinmin ; Green, Roland ; Farnham, Peggy J. / Genome-scale ChIP-chip analysis using 10,000 human cells. In: BioTechniques. 2007 ; Vol. 43, No. 6. pp. 791-797.
@article{ffac860ef3164dd7a5c1f692f4fec5b1,
title = "Genome-scale ChIP-chip analysis using 10,000 human cells",
abstract = "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.",
author = "Acevedo, {Luis G.} and Iniguez, {A. Leonardo} and Holster, {Heather L.} and Xinmin Zhang and Roland Green and Farnham, {Peggy J.}",
year = "2007",
month = "12",
doi = "10.2144/000112625",
language = "English (US)",
volume = "43",
pages = "791--797",
journal = "BioTechniques",
issn = "0736-6205",
publisher = "Eaton Publishing Company",
number = "6",

}

TY - JOUR

T1 - Genome-scale ChIP-chip analysis using 10,000 human cells

AU - Acevedo, Luis G.

AU - Iniguez, A. Leonardo

AU - Holster, Heather L.

AU - Zhang, Xinmin

AU - Green, Roland

AU - Farnham, Peggy J.

PY - 2007/12

Y1 - 2007/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=37349081961&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=37349081961&partnerID=8YFLogxK

U2 - 10.2144/000112625

DO - 10.2144/000112625

M3 - Article

C2 - 18251256

AN - SCOPUS:37349081961

VL - 43

SP - 791

EP - 797

JO - BioTechniques

JF - BioTechniques

SN - 0736-6205

IS - 6

ER -