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DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.

Publication ,  Journal Article
Crawford, GE; Davis, S; Scacheri, PC; Renaud, G; Halawi, MJ; Erdos, MR; Green, R; Meltzer, PS; Wolfsberg, TG; Collins, FS
Published in: Nat Methods
July 2006

Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including promoters, enhancers, silencers and locus control regions. Although Southern blots are the traditional method of identifying DNase I hypersensitive sites, the conventional manual method is not readily scalable to studying large chromosomal regions, much less the entire genome. Here we describe DNase-chip, an approach that can rapidly identify DNase I hypersensitive sites for any region of interest, or potentially for the entire genome, by using tiled microarrays. We used DNase-chip to identify DNase I hypersensitive sites accurately from a representative 1% of the human genome in both primary and immortalized cell types. We found that although most DNase I hypersensitive sites were present in both cell types studied, some of them were cell-type specific. This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome.

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Published In

Nat Methods

DOI

ISSN

1548-7091

Publication Date

July 2006

Volume

3

Issue

7

Start / End Page

503 / 509

Location

United States

Related Subject Headings

  • Sensitivity and Specificity
  • Regulatory Sequences, Nucleic Acid
  • Oligonucleotide Array Sequence Analysis
  • Humans
  • Gene Expression Profiling
  • Developmental Biology
  • Deoxyribonuclease I
  • Cells, Cultured
  • 31 Biological sciences
  • 11 Medical and Health Sciences
 

Citation

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Crawford, G. E., Davis, S., Scacheri, P. C., Renaud, G., Halawi, M. J., Erdos, M. R., … Collins, F. S. (2006). DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods, 3(7), 503–509. https://doi.org/10.1038/nmeth888
Crawford, Gregory E., Sean Davis, Peter C. Scacheri, Gabriel Renaud, Mohamad J. Halawi, Michael R. Erdos, Roland Green, Paul S. Meltzer, Tyra G. Wolfsberg, and Francis S. Collins. “DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.Nat Methods 3, no. 7 (July 2006): 503–9. https://doi.org/10.1038/nmeth888.
Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, et al. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503–9.
Crawford, Gregory E., et al. “DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.Nat Methods, vol. 3, no. 7, July 2006, pp. 503–09. Pubmed, doi:10.1038/nmeth888.
Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503–509.

Published In

Nat Methods

DOI

ISSN

1548-7091

Publication Date

July 2006

Volume

3

Issue

7

Start / End Page

503 / 509

Location

United States

Related Subject Headings

  • Sensitivity and Specificity
  • Regulatory Sequences, Nucleic Acid
  • Oligonucleotide Array Sequence Analysis
  • Humans
  • Gene Expression Profiling
  • Developmental Biology
  • Deoxyribonuclease I
  • Cells, Cultured
  • 31 Biological sciences
  • 11 Medical and Health Sciences