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Links from GEO DataSets

Items: 20

1.

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [Affymetrix]

(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
Series
Accession:
GSE41770
ID:
200041770
2.

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

(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
Series
Accession:
GSE41773
ID:
200041773
3.

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [NGS_Illumina]

(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
Series
Accession:
GSE41772
ID:
200041772
4.

Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

(Submitter supplied) In Schizosaccharomyces pombe, DNA replication origins (ORIs) and meiotic recombination hotspots lack consensus sequences and show a bias towards mapping at large intergenic regions (IGRs). To explore whether this preference depended on underlying chromatin features, we have generated genome-wide nucleosome profiles during mitosis and meiosis. We have found that meiotic double-strand break sites (DSB) colocalize strictly with nucleosome-depleted regions (NDRs) and that large IGRs include clusters of NDRs that overlap with almost half of all DSBs. more...
Organism:
Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL7715
10 Samples
Download data: CEL, WIG
Series
Accession:
GSE28879
ID:
200028879
5.

S. pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from S. cerevisiae

(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
Series
Accession:
GSE16040
ID:
200016040
6.

High-resolution nucleosome positioning from ATAC-seq chromatin accessibility data

(Submitter supplied) We describe the NucleoATAC algorithm for high-resolution nucleosome positioning and occupancy determination using ATAC-seq.
Organism:
Schizosaccharomyces pombe; Saccharomyces cerevisiae; Homo sapiens
Type:
Other
4 related Platforms
32 Samples
Download data
Series
Accession:
GSE66386
ID:
200066386
7.

Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome

(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
Series
Accession:
GSE29294
ID:
200029294
8.

Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [RNA_seq]

(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
Series
Accession:
GSE29293
ID:
200029293
9.

Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [Paired-end Mnase-seq]

(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
Series
Accession:
GSE29292
ID:
200029292
10.

Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [single-end MNase-seq]

(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
Series
Accession:
GSE29291
ID:
200029291
11.

RSC Defines MNase-sensitive Promoter Architecture in Yeast

(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
Series
Accession:
GSE116853
ID:
200116853
12.

Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome

(Submitter supplied) In the yeast genome, a large proportion of nucleosomes occupy well-defined positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genomic context remains controversial. Through genome-wide, quantitative analysis of nucleosome positioning and high-resolution mutagenenesis of mononucleosomal DNA, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes. more...
Organism:
Saccharomyces cerevisiae; Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19756 GPL20584
46 Samples
Download data: WIG
Series
Accession:
GSE84910
ID:
200084910
13.

The conserved role of the RSC chromatin remodeler in the establishment of nucleosome depleted regions

(Submitter supplied) The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodeling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. more...
Organism:
Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20584
4 Samples
Download data: WIG
Series
Accession:
GSE84912
ID:
200084912
14.

Mechanisms that specify promoter nucleosome location and identity

(Submitter supplied) The chromatin architecture of eukaryotic gene promoters is generally characterized by a nucleosome-free region (NFR) flanked by at least one H2A.Z variant nucleosome. Computational predictions of nucleosome positions based on thermodynamic properties of DNA-histone interactions have met with limited success. Here we show that the action of the essential RSC remodeling complex in S. cerevisiae helps explain the discrepancy between theory and experiment. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array; Expression profiling by array
Platforms:
GPL7542 GPL7550
66 Samples
Download data: GPR
Series
Accession:
GSE13446
ID:
200013446
15.

CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5’ ends of genes in S. Pombe

(Submitter supplied) Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5’ end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pervasive pattern are unclear, but nucleosome remodeling ATPases likely are critical. Now we employ deletion mutants to study the role of nucleosome remodeling ATPases in global nucleosome positioning in S. more...
Organism:
Schizosaccharomyces pombe
Type:
Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array
Platform:
GPL7715
40 Samples
Download data: CEL, TXT
Series
Accession:
GSE41024
ID:
200041024
16.

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

(Submitter supplied) Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13821
11 Samples
Download data: WIG
Series
Accession:
GSE39431
ID:
200039431
17.

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)

(Submitter supplied) Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13821
7 Samples
Download data: WIG
Series
Accession:
GSE39430
ID:
200039430
18.

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Genome variation profiling by high throughput sequencing
Platform:
GPL13821
18 Samples
Download data: WIG
Series
Accession:
GSE39331
ID:
200039331
19.

Chemical map of S. pombe reveals species-specific features in nucleosome positioning

(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
Series
Accession:
GSE46975
ID:
200046975
20.

A genome wide role for CHD remodeling factors and Nap1 in nucleosome disassembly

(Submitter supplied) Chromatin remodeling factors and histone chaperones were previously shown to cooperatively affect nucleosome assembly and disassembly processes in vitro. Here we show that S. pombe CHD remodellers, Hrp1 and Hrp3 physically interact with the histone chaperone Nap1. Genome wide analysis of Hrp1, Hrp3 and Nap1 occupancy, combined with nucleosome density measurements in respective mutants revealed that the CHD factors and Nap1 co-localized in particular to promoter regions where they remove nucleosomes near the transcriptional start site. more...
Organism:
Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by array; Genome binding/occupancy profiling by genome tiling array
9 related Platforms
54 Samples
Download data: CEL, TXT, XLS
Series
Accession:
GSE6557
ID:
200006557
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