GEO DataSets

(Submitter supplied) To measure nucleosome positions on a genomic scale, we developed a high-throughput DNA microarray method to identify nucleosomal and linker DNA sequences based on susceptibility of linker DNA to micrococcal nuclease. Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1950

8 Samples

Download data

(Submitter supplied) Study to detect to genome wide localization of the ATP dependent chromatin remodelling factor Isw2 using ChIP. Keywords: ChIP chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6476

6 Samples

Download data: CEL

(Submitter supplied) To map nucleosome positions in WT and delta isw2 cells Keywords: Nucleosomal DNA hybridization

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6476

8 Samples

Download data: CEL

(Submitter supplied) To define chromatin structure changes along the yeast genome using microarrays. Nucleosomal DNA from WT and delta isw2 yeast were hybridized and differences in signals were calculated. Keywords: Nucleosomal DNA hybridization

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6476

4 Samples

Download data: CEL

(Submitter supplied) In yeast cells, preferential accessibility of the HIS3-PET56 promoter region is determined by a general property of the DNA sequence, not by defined sequence elements. In vivo, this region is largely devoid of nucleosomes, and accessibility is directly related to reduced histone density. The HIS3-PET56 and DED1 promoter regions associate poorly with histones in vitro, indicating that intrinsic nucleosome positioning and stability is a major determinant of preferential accessibility. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL2045 GPL2046

6 Samples

Download data: GPR

(Submitter supplied) The identification of nuclease-hypersensitive sites in an active globin gene and in the 5' regions of fruit fly heat shock genes first suggested that chromatin changes accompany gene regulation in vivo. Here we present evidence that the basic repeating units of eukaryotic chromatin, nucleosomes, are depleted from active regulatory elements throughout the Saccharomyces cerevisiae genome in vivo. We found that during rapid mitotic growth, the level of nucleosome occupancy is inversely proportional to the transcriptional initiation rate at the promoter. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3704

24 Samples

Download data: GPR

(Submitter supplied) Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes. Here we generated the first genome-wide nucleosome positioning map for Schizosaccharomyces pombe and annotated transcription start and termination sites genome-wide. Using this resource we found surprising differences compared to the nucleosome organization in the distantly related yeast Saccharomyces cerevisiae [the cerevisiae data has been published by others (PMID: 17873876) and the raw data is deposited at ArrayExpress(E-MEXP-1172)]. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:

GPL7715 GPL2529

16 Samples

Download data: BAR, CEL

(Submitter supplied) We describe the NucleoATAC algorithm for high-resolution nucleosome positioning and occupancy determination using ATAC-seq.

Organism:

Saccharomyces cerevisiae; Homo sapiens; Schizosaccharomyces pombe

Type:

Other

4 related Platforms

32 Samples

Download data

(Submitter supplied) Genome wide interaction of mediator Keywords: Genome wide interaction of mediator

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL2789 GPL2795 GPL3592

36 Samples

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(Submitter supplied) Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation as nucleosomes modulate DNA access by their positioning along the genome. A cell population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods as they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or non-nucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18085

78 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation as nucleosomes modulate DNA access by their positioning along the genome. A cell population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods as they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or non-nucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18085

83 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation as nucleosomes modulate DNA access by their positioning along the genome. A cell population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods as they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or non-nucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25739

2 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation as nucleosomes modulate DNA access by their positioning along the genome. A cell population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods as they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or non-nucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18085

1 Sample

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25739 GPL18085

164 Samples

Download data: BEDGRAPH, TSV

(Submitter supplied) Knowing the exact positions of nucleosomes not only advances our understanding of their role in gene regulation, but also the mechanisms that underlie between-species variation in chromatin structure. We have generated a chemical map of nucleosomes in vivo in Schizosaccharomyces pombe at base pair resolution. This new map reveals that S.pombe genome shares a similar periodic linker length distribution with Saccharomyces cerevisiae, but with major distinctions in nucleosomal/linker DNA sequence features. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platforms:

GPL17165 GPL17205

2 Samples

Download data: TXT

(Submitter supplied) Previous studies indicate that eukaryotic promoters display a stereotypical chromatin landscape characterized by a well-positioned +1 nucleosome near the transcription start site and an upstream -1 nucleosome that together demarcate a nucleosome-free (or depleted) region. Here we present evidence that there are two distinct types of promoters distinguished by the resistance of the -1 nucleosome to micrococcal nuclease digestion. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

32 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by genome tiling array

Platforms:

GPL7715 GPL15167

15 Samples

Download data: CEL, WIG

(Submitter supplied) Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe.

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15167

5 Samples

Download data: WIG

(Submitter supplied) Mononucleosomal DNA analysis of atf1D and pcr1D mutants of Schizosaccharomyces pombe and transcription analysis of exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114, and synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array

Platform:

GPL7715

10 Samples

Download data: CEL, WIG

(Submitter supplied) We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

5 Samples

Download data: TXT