Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique
Mapping sites within the genome that are hypersensitive to digestion with DNaseI is an important method for identifying DNA elements that regulate transcription. The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has been to use Southern blotting techniques, although we, and...
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| Format: | Online |
| Language: | English |
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Oxford University Press
2007
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885650/ |
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pubmed-1885650 |
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oai_dc |
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pubmed-18856502007-06-07 Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique Follows, George A. Janes, Mary E. Vallier, Ludovic Green, Anthony R. Gottgens, Berthold Methods Online Mapping sites within the genome that are hypersensitive to digestion with DNaseI is an important method for identifying DNA elements that regulate transcription. The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has been to use Southern blotting techniques, although we, and others, have recently published alternative methods using a range of technologies including high-throughput sequencing and genomic array tiling paths. In this article, we describe a novel protocol to use real-time PCR to map DHS. Advantages of the technique reported here include the small cell numbers required for each analysis, rapid, relatively low-cost experiments with minimal need for specialist equipment. Presented examples include comparative DHS mapping of known TAL1/SCL regulatory elements between human embryonic stem cells and K562 cells. Oxford University Press 2007-04 2007-03-27 /pmc/articles/PMC1885650/ /pubmed/17389645 http://dx.doi.org/10.1093/nar/gkm108 Text en © 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Follows, George A. Janes, Mary E. Vallier, Ludovic Green, Anthony R. Gottgens, Berthold |
| spellingShingle |
Follows, George A. Janes, Mary E. Vallier, Ludovic Green, Anthony R. Gottgens, Berthold Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique |
| author_facet |
Follows, George A. Janes, Mary E. Vallier, Ludovic Green, Anthony R. Gottgens, Berthold |
| author_sort |
Follows, George A. |
| title |
Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique |
| title_short |
Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique |
| title_full |
Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique |
| title_fullStr |
Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique |
| title_full_unstemmed |
Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique |
| title_sort |
real-time pcr mapping of dnasei-hypersensitive sites using a novel ligation-mediated amplification technique |
| description |
Mapping sites within the genome that are hypersensitive to digestion with DNaseI is an important method for identifying DNA elements that regulate transcription. The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has been to use Southern blotting techniques, although we, and others, have recently published alternative methods using a range of technologies including high-throughput sequencing and genomic array tiling paths. In this article, we describe a novel protocol to use real-time PCR to map DHS. Advantages of the technique reported here include the small cell numbers required for each analysis, rapid, relatively low-cost experiments with minimal need for specialist equipment. Presented examples include comparative DHS mapping of known TAL1/SCL regulatory elements between human embryonic stem cells and K562 cells. |
| publisher |
Oxford University Press |
| publishDate |
2007 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885650/ |
| _version_ |
1611396920570281984 |