GEO DataSets

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

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL13272

20 Samples

Download data: BED, TXT, WIG

(Submitter supplied) Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13272

6 Samples

Download data: WIG

(Submitter supplied) Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

8 Samples

Download data: BED, TXT

(Submitter supplied) Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

6 Samples

Download data: BED, TXT

(Submitter supplied) Understanding chromatin dynamics is a key to other related processes, including DNA replication, transcription and recombination. As a first step, recently, an increasing amount of effort has been devoted to precisely define nucleosome positioning in different organisms. The most popular method to do so is digestion by Micrococcal nuclease (MNase), nowadays followed by ultrasequencing of the generated fragments. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13821 GPL13272

3 Samples

Download data: BED

(Submitter supplied) We have developed a new genome-wide protocol for nascent transcription analysis at high resolution in the yeast Saccharomyces cerevisiae. This protocol is based in run-on labeling of nascent RNA with a biotinylated precursor. We call it BioGRO for biotin-based genomic run-on.

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL18871

7 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) In order to maintain the appropriate level of mRNA it is necessary coordinate simultaneously all the steps along the mRNA life cycle. It has been shown that several factors act in the regulation of gene expression as global coordinators. Thus, some kind of information is transferred from the nucleus to the cytoplasm, imprinted in the mRNA. In this way, it is conceivable the existence of mechanisms that ensure the balance between mRNA synthesis and degradation through the information flow from the cytoplasm to the nucleus and vice versa, as a crosstalk among both process to ensure the proper mRNA homeostasis in the cell. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13620

18 Samples

Download data: TXT

(Submitter supplied) Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that nucleosomes at 5% of budding yeast nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17342 GPL13821

17 Samples

Download data: BED

(Submitter supplied) The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome center positions genome-wide in unprecedented detail and accuracy. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL15263

6 Samples

Download data: TXT

(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:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

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

Platforms:

GPL7715 GPL2529

16 Samples

Download data: BAR, CEL

(Submitter supplied) Intact nuclei from an asynchronous population of W303 Saccharomyces cerevisiae in log-phase growth were subjected to a 16-minute DNase I digestion (0.1 U/μL) at 37 °C. DNA was then recovered, and single-end Illumina sequencing libraries were prepared using the Crawford DNase-seq method (Song and Crawford, 2010).

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

2 Samples

Download data: CSV

(Submitter supplied) The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently challenged by contradictory reports as to whether a distinct set of wider (≳150 bp) NDRs instead contain unusually unstable Micrococcal Nuclease-sensitive “fragile” particles, thought to be nucleosomal because of their size. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

63 Samples

Download data: BEDGRAPH, PDF

(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) 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:

GPL17205 GPL17165

2 Samples

Download data: TXT