GEO DataSets

(Submitter supplied) Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

38 Samples

Download data: BW, TXT

(Submitter supplied) Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

14 Samples

Download data: BW

(Submitter supplied) Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

10 Samples

Download data: BW

(Submitter supplied) Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

3 Samples

Download data: TXT

(Submitter supplied) Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this compatibility has remained poorly characterised in mammalian cells. By systematic reporter assays of thousands of CRE – promoter pairs from three Mb-sized genomic regions in mouse cells, we found that CREs vary substantially in their promoter compatibility, with more than half showing significant selectivity. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL17021 GPL16417

46 Samples

Download data: TSV

(Submitter supplied) Ki67 is a widely-used proliferation marker with functions in chromosomal organization. It forms a protective layer around mitotic chromosomes and is involved in genome positioning in interphase. However, a detailed understanding of how Ki67 organizes the genome was still lacking, partially because genome-wide interaction profiles were missing. Here, we generate DNA-Ki67 interaction profiles using our pA-DamID method, and show that Ki67 interacts with the genome in a domain-like pattern that partially overlaps with lamina-associated domains.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL16791

213 Samples

Download data: BED, BW, MATRIX, TSV

(Submitter supplied) Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL17021

14 Samples

Download data: BED, BW, NARROWPEAK

(Submitter supplied) Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

116 Samples

Download data: BW, TSV

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

Organism:

Mus musculus

Type:

Other

Platforms:

GPL17021 GPL24973 GPL19057

23 Samples

Download data: MATRIX, TXT

(Submitter supplied) Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

1 Sample

Download data: TXT

(Submitter supplied) Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

18 Samples

Download data: MATRIX, TXT

(Submitter supplied) Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.

Organism:

Mus musculus

Type:

Other

Platform:

GPL24973

1 Sample

Download data

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL16791

29 Samples

Download data: BW

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: BW

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: BW

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: HIC, TXT

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

Organism:

Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum

Type:

Other

30 related Platforms

32 Samples

Download data: BEDPE, FASTA, HIC, VCF, WIG

(Submitter supplied) We used DamID to map nucleolus interactions in human cells using a 4x tandem repeat of the nucleolar targeting sequence of AP3D1 (Scott, 2010) ("4xAP3"). These interactions are mapped in various human cell lines, including human K562 cells

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

8 Samples

Download data: BW

(Submitter supplied) This study addresses the mechanisms regulating the identity of oligodendrocyte progenitor cells (OPC) in physiological conditions and the pathological mechanisms leading to autosomal  adrenoleukodystrophy (ADLD), a disease caused by persistence of lamin B1 (LMNB1) expression in oligodendrocytes (OL).  Using mouse primary OPCs and a novel technique for the study of DNA-protein interaction, we identify the genomic regions showing dynamic interactions with LMNB1.  The transition from ESC to OPC revealed increased association of gene involved in pluripotency and neuronal function and decreased association of gene categories associated with the differentiation of OPC into OL (including genes regulating epigenetic modifiers, RNA processing and protein phosphorylation).  Since LMNB1 declines during the transition from OPC to OL, and its persistent expression has been linked to pathological conditions, such as ADLD, we further identified the molecular maps of genome-lamina reorganization in OPC differentiating into OL which continue to express LMNB1 (mOLLMNB1).  The transition from OPC to mOLLMNB1 revealed increased association to LMNB1 of genomic regions encoding for lipid metabolism and protein phosphorylation, and decreased association of genes negatively regulating differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

11 Samples

Download data: BW, TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL16791 GPL17021

174 Samples

Download data: TXT