GEO DataSets

(Submitter supplied) The nuclear lamina (NL) interacts with hundreds of large genomic regions termed lamina-associated domains (LADs). The dynamics of these interactions and the relation to epigenetic modifications are poorly understood. We visualized the fate of LADs in single cells using a novel 'molecular contact memory' approach. In each interphase nucleus, only ~30% of LADs are positioned at the periphery; these LADs are in intermittent molecular contact with the NL but remain constrained to the periphery. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL10559

1 Sample

Download data: PAIR

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL10559

13 Samples

Download data: PAIR

(Submitter supplied) The nuclear lamina (NL) interacts with hundreds of large genomic regions termed lamina-associated domains (LADs). The dynamics of these interactions and the relation to epigenetic modifications are poorly understood. We visualized the fate of LADs in single cells using a novel 'molecular contact memory' approach. In each interphase nucleus, only ~30% of LADs are positioned at the periphery; these LADs are in intermittent molecular contact with the NL but remain constrained to the periphery. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

2 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL11154 GPL10559

411 Samples

Download data: PAIR

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10559

2 Samples

Download data: PAIR

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: CSV, TXT

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

52 Samples

Download data: TXT

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

124 Samples

Download data: TXT

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

26 Samples

Download data: TXT

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

35 Samples

Download data: TXT

(Submitter supplied) Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

172 Samples

Download data: TXT

(Submitter supplied) Proper genome functionality is underpinned by the non-random, spatial or ganisation of chromatin. At the periphery of the nucleus, the association of chr omatin with the nuclear lamina is thought to facilitate both structural organisa tion and regulation of gene expression. Except for a small number of individual loci, the regions of the human genome that locate at the nuclear lamina have not been identified. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

9 related Platforms

10 Samples

Download data: TSV, TXT

(Submitter supplied) The nuclear lamina (NL) is a filamentous layer lining the inner-nuclear-membrane (INM) that aids in the organization of the genome in large domains of low transcriptional activity. Recently, it was shown that the single-cell genome-NL interactions are much more dynamic than previously anticipated, which challenges the concept of the NL as a safe guard for transcriptional repressed genes. Here we discuss the role of the NL in light of these new findings and introduce Lamin A and BAF as potential modulators of LAD positioning

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10559

4 Samples

Download data: PAIR, 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:

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) We have used microarrays to identify LaminB1 occupancy signal in AML12 cell using the DamID protocol.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10448

4 Samples

Download data: TXT

(Submitter supplied) We asked if the perinuclear position of chromosome arms in C. elegans depends on the histone methyltransferases MET-2 and SET-25. To this end, we performed LMN-1-DamID in wild-type (N2) and mutant (set-25 met-2) strains. LMN-1-DamID signal on chromosome arms was significantly reduced in the mutant.

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL8134

6 Samples

Download data: PAIR, TAB

(Submitter supplied) Nuclear compartmentalization appears to play an important role in regulating metazoan genes. While studies on immunoglobulin (Ig) and other loci have correlated positioning at the nuclear lamina with gene repression, the functional consequences of this compartmentalization remain untested. We devised an approach for inducible tethering of genes to the inner nuclear membrane (INM) and demonstrate with 3D DNA-ImmunoFISH, repositioning of chromosomal regions to the nuclear lamina. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL