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Genome access is transcription factor specific and defined by nucleosome position [ChIP-Seq]

ABSTRACT: Genome access is transcription factor specific and defined by nucleosome position [ChIP-Seq]

PROVIDER: PRJNA1004564 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25610033_1.fastq.gz	Fastqsanger.gz
	SRR25610033_2.fastq.gz	Fastqsanger.gz
	SRR25610034_1.fastq.gz	Fastqsanger.gz
	SRR25610034_2.fastq.gz	Fastqsanger.gz
	SRR25610035_1.fastq.gz	Fastqsanger.gz

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Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Anshul Kundaje mailto:akundaje@stanford.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). Nucleosomes are part of the first level of chromatin packaging. They each consist of a histone heterooctamer around which DNA wraps 1.6 times. The histone heterooctomamer is made up of two copies of histones 2A, 2B, 3 and 5. The segment of DNA wrapped around the histones, the so-called "core" fragment, is 147 base pairs long. Neighboring nucleosomes are separated from one another by a stretch of DNA called the "linker," whose size varies depending on organism, cell type, and even chromatin activity. Certain chromatin remodeling factors govern accessibility of DNA to regulatory proteins by repositioning nucleosomes to reveal regulatory sites that would otherwise be occluded by a nucleosome. In contrast to histone modifications such as methylation or acetylation, which are investigated by ChIP-seq, nucleosome positioning data are generated without immunoprecipitation (see Methods below). Instead, micrococcal nuclease is used to digest chromatin to apparent completion, the (well-defined and clearly visible) mononucleosomal core fragment fraction is isolated by gel purification, and one end is then sequenced. Mapping the sequence tag back to the genome reveals the precise position of one end of the core fragment that was protected by the nucleosome; the position of the other end can then simply be inferred by extending the read to a virtual length of 147 bases. Statistical analyses such as occupancy and positioning stringency can then be employed to analyze the local nucleosome landscape anywhere in the (mappable) genome or to infer global parameters of nucleosome organization. In the context of the ENCODE project, nucleosome positioning data are particularly valuable for analysis of the relationship between transcription factor binding, histone modifications, and gene activity. For a general primer on these types of data and analyses, refer to Valouev et al. (2008). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

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Genome access is transcription factor specific and defined by nucleosome position [ChIP-Seq]

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