GEO DataSets

(Submitter supplied) CAF-1 is a major nucleosome assembly complex, which functions particularly during replication and DNA-repair. Here, we studied how the nucleosome landscape changes in fas2 a mutant of the CAF-1 complex in the model plant Arabidopsis thaliana

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: BED, TSV

(Submitter supplied) Comparative study of nuclesome occupancy in Arabidopsis thaliana mutant chr5 and wild type strain.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: BED

(Submitter supplied) Background: Analysis of the effect that chromatin structure has on the expression patterns of eukaryotic genes has recently expanded knowledge of the complex influence genome accessibility has on genome function. Interlaced with regular nucleosomal patterning are other mobile and labile sub-nucleosomal-sized protein structures bound to the genome such as transcription factors (TF), initiation complexes, and modified nucleosomes. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

16 Samples

Download data: CSV, WIG

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL9377 GPL7070

185 Samples

Download data: BAR, CEL, WIG

(Submitter supplied) Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

16 Samples

Download data: WIG

(Submitter supplied) Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7070

107 Samples

Download data: BAR, CEL

(Submitter supplied) Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL7070

62 Samples

Download data: BAR, CEL

(Submitter supplied) Chromatin has a highly organized structure with the repeating nucleosome subunits. The position of nucleosomes on the chromatin is dynamically regulated by ATP-dependent chromatin remodeling factors (remodelers), therefore providing specific epigenetic information. However, the in vivo nucleosome distribution pattern in plants and how plant remodelers control the pattern formation are not yet clear. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17639

2 Samples

Download data: WIG

(Submitter supplied) Affymetrix expression analysis was used to validate the role of NPR1 in SA mediated transcription.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

8 Samples

Download data: CEL, CHP

(Submitter supplied) Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with the Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

40 Samples

Download data: BW

(Submitter supplied) We report the global nuclesome posiitons to study the relationship between nucleosome occupancy and gene expression in response to Coronatine in Arabidopsis

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

9 Samples

Download data: TXT

(Submitter supplied) Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. more...

Organism:

Arabidopsis thaliana; Homo sapiens

Type:

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

Platforms:

GPL9062 GPL9302 GPL9115

4 Samples

Download data: TXT

(Submitter supplied) Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer1, 2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10978 GPL10977

2 Samples

Download data: BAR, CEL

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

Organism:

Homo sapiens; Arabidopsis thaliana

Type:

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

5 related Platforms

6 Samples

Download data: CEL, 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) We assess global chromatin accessibility following high salt wash

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

2 Samples

Download data: BW

(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

(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