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DNase-chip: A High Resolution Method to Identify DNaseI Hypersensitive Sites using Tiled Microarrays
Gregory E. Crawford1,3, Sean Davis1, Peter C. Scacheri1, Gabriel Renaud1, Mohamad J. Halawi1, Michael R. Erdos1, Roland Green2, Paul S. Meltzer1, Tyra G. Wolfsberg1, and Francis S. Collins1
1National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
2NimbleGen Systems, Incorporated, Madison, WI 53711
3Present address: Institute for Genome Sciences & Policy, and Department of Pediatrics, 101 Science Drive, CIEMAS Building, Duke University, Box 3382, Durham, North Carolina 27708
Abstract
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.
Data
Data are mapped using human hg16 and hg17 coordinates. Data are only from ENCODE regions.
DNAse HS sites were assayed in two cell types, human primary CD4+ T cells and the GM06990 lymphoblastoid cell line. Cells were treated with three concentrations of DNAse (Conc A, B, and C). Each assay was performed using 3 biological replicates; the data below are the result of averaging the replicates. Conc_ABC_averaged is the result of averaging the replicates over all three DNase concentrations.
We are providing the raw ratio data, as well as processed data. Processed data are regions that display significant signal (in addition, -log10 pvalues are supplied) using the Algorithm for Capturing Microarray Enrichment (ACME; see paper for details).
Conc_A equals 0.4U DNase
Conc_B equals 1.2U DNase
Conc_C equals 4.0U DNase
| CD4+ T cells | | GM06990 lymphoblastoid cell line |
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(These coordinates were converted from hg16 to hg17 using the UCSC LiftOver program.)
| CD4+ T cells | | GM06990 lymphoblastoid cell line |
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