GEO DataSets

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

Organism:

Escherichia coli; Methanothermus fervidus

Type:

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

Platforms:

GPL18133 GPL16085 GPL26241

74 Samples

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(Submitter supplied) Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically widespread but not universal: several archaeal lineages have independently lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we use micrococcal nuclease digestion of native and reconstituted chromatin to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. more...

Organism:

Escherichia coli; Thermoplasma acidophilum; synthetic construct

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL19604 GPL18133 GPL26243

12 Samples

Download data: BW

(Submitter supplied) Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

50 Samples

Download data: CSV

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

Organism:

synthetic construct; Escherichia coli; Thermoplasma acidophilum

Type:

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

Platforms:

GPL26243 GPL19604 GPL18133

51 Samples

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(Submitter supplied) We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. more...

Organism:

Thermoplasma acidophilum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26243

23 Samples

Download data: BED

(Submitter supplied) We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. more...

Organism:

Thermoplasma acidophilum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26243

16 Samples

Download data: CSV, XLSX

(Submitter supplied) Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16085

18 Samples

Download data: BW

(Submitter supplied) Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. more...

Organism:

Methanothermus fervidus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26241

6 Samples

Download data: BW

(Submitter supplied) Diverse studies including protemoics, genome-wide binding, and transcriptional profiling of the model halophile Halobacterium salinarum suggest that its putative histone protein acts not as a chromatin protein but a direct and indirect transcriptional regulator. Here, we characterise the putative histone (HstA) of another model halophile (Haloferax volcanii) with ChIP-Seq to understand its genome-wide binding, and compare it with binding patterns seen from histones, nucleoid-associated proteins, and transcription factors of Halobacterium salinarum, other archaea, and eukaryotes. more...

Organism:

Haloferax volcanii DS2

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30888

8 Samples

Download data: WIG

(Submitter supplied) Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ~147 bp of DNA wrapped ~1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. more...

Organism:

Mus musculus; Saccharomyces cerevisiae; Synthetic plasmid

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

31 Samples

Download data: BW, FA, TXT

(Submitter supplied) We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent. To this end, gene expression data for a histone knock-out (Δura3ΔhpyA) strain versus parent (Δura3) were collected.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL14876

12 Samples

Download data: TXT

(Submitter supplied) Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone-DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. more...

Organism:

Caenorhabditis elegans

Type:

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

Platform:

GPL18245

24 Samples

Download data: BED, BW, TXT

(Submitter supplied) Histones are the primary building blocks of chromatin in eukaryotes and many archaea. Bacteria are thought to rely on an orthogonal set of proteins to organize their chromosomes. Several bacterial genomes do, however, encode proteins with putative histone fold domains. Whether these proteins adopt a bona fide histone fold, assemble into higher order complexes that bind DNA, and play a central role in bacterial nucleoid physiology is not known. more...

Organism:

Bdellovibrio bacteriovorus; Aquifex aeolicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25581 GPL28567

5 Samples

Download data: TXT

(Submitter supplied) Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal configuration of such open chromatin and the basis for chromatin opening is unclear. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: BW

(Submitter supplied) Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal status of such open chromatin, e.g., at active enhancers, is not clear. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057

54 Samples

Download data: BED, BW

(Submitter supplied) In higher eukaryotes, enhancers and promoters share many properties, including binding of transcription factors, existing in open chromatin, and bidirectional transcription. Yet the structural features that distinguish enhancers and promoters are unclear. Genome-wide micrococcal nuclease (MNase) studies previously interpreted MNase hypersensitivity to indicate that active enhancers and promoters are nucleosome-free, yet other studies found histone variants and post-translational modifications at active enhancers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BED, BW

(Submitter supplied) In higher eukaryotes, enhancers and promoters share many properties, including binding of transcription factors, existing in open chromatin, and bidirectional transcription. Yet the structural features that distinguish enhancers and promoters are unclear. Genome-wide micrococcal nuclease (MNase) studies previously interpreted MNase hypersensitivity to indicate that active enhancers and promoters are nucleosome-free, yet other studies found histone variants and post-translational modifications at active enhancers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BED, BW

(Submitter supplied) In higher eukaryotes, enhancers and promoters share many properties, including binding of transcription factors, existing in open chromatin, and bidirectional transcription. Yet the structural features that distinguish enhancers and promoters are unclear. Genome-wide micrococcal nuclease (MNase) studies previously interpreted MNase hypersensitivity to indicate that active enhancers and promoters are nucleosome-free, yet other studies found histone variants and post-translational modifications at active enhancers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BED

(Submitter supplied) Chromatin accessibility plays a fundamental role in gene regulation. One mechanism to regulate accessibility is nucleosome placement, which is often measured by quantifying protection of DNA from enzymatic digestion. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. more...

Organism:

Homo sapiens; Mus musculus; Drosophila melanogaster

Type:

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

Platforms:

GPL16791 GPL17275 GPL17021

74 Samples

Download data: BEDGRAPH