GEO DataSets

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...

Organism:

Mus musculus x Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20213

6 Samples

Download data: BED, XLS

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...

Organism:

Mus musculus x Mus spretus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20213

17 Samples

Download data: TSV

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...

Organism:

Mus musculus x Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20213

4 Samples

Download data: BED, XLS

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...

Organism:

Mus musculus x Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20213

6 Samples

Download data: TXT

(Submitter supplied) In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. Results We find radically different conformations for the two female mouse X chromosomes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10129

2 Samples

Download data: GFF

(Submitter supplied) A subset of genomic regions, including one of the female X chromosomes and all imprinted genes, are expressed exclusively from a single allele in somatic cells of mammals. To evaluate structural changes associated with allelic silencing, we used mouse F1 hybrid systems in which X inactivation is skewed and alleles can be distinguished based on single nucleotide polymorphisms to analyze chromatin contacts by a new Hi-C assay that uses DNase I for chromatin fragmentation. more...

Organism:

Mus musculus x Mus spretus

Type:

Other

Platforms:

GPL16616 GPL20213

4 Samples

Download data: TXT

(Submitter supplied) In mammals, genes located on the X chromosome are present in one copy in XY males and two in XX females. To balance the dosage of X-linked gene expression between the sexes one of the two X chromosomes in females is silenced by X inactivation initiated by up-regulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers for silencing. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. more...

Organism:

Mus musculus x Mus spretus; Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

5 related Platforms

19 Samples

Download data: GFF, PAIR

(Submitter supplied) In mammals, genes located on the X chromosome are present in one copy in XY males and two in XX females. To balance the dosage of X-linked gene expression between the sexes one of the two X chromosomes in females is silenced by X inactivation initiated by up-regulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers for silencing. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. more...

Organism:

Mus musculus x Mus spretus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16617

4 Samples

Download data: TXT

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

Organism:

Mus musculus; Mus musculus x Mus spretus

Type:

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

9 related Platforms

70 Samples

Download data: BED, BIGWIG, GFF, PAIR, TXT, XLS

(Submitter supplied) X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape gene in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. more...

Organism:

Mus musculus x Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18997 GPL16617

3 Samples

Download data: BED, BIGWIG

(Submitter supplied) X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape gene in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. more...

Organism:

Mus musculus x Mus spretus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16617

5 Samples

Download data: TXT

(Submitter supplied) Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). more...

Organism:

Mus musculus; Mus musculus x Mus spretus

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10129 GPL16733 GPL16143

25 Samples

Download data: PAIR

(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNA polymerase II phosphorylated at serine 5 (PolII-S5p; the transcription initiation form) in female mouse cultured hybrid cells and female hybrid brain derived from mouse systems with skewed X inactivation based on crosses between C57BL/6J (BL6) and M. spretus. In these systems, alleles can be differentiated by frequent SNPs between mouse species, and the active X (Xa) compared to the haploid set of autosomes from the same species. more...

Organism:

Mus musculus x Mus spretus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16616 GPL16617

3 Samples

Download data: BED, BIGWIG

(Submitter supplied) To address the functional role of MOF in mammalian X upregulation, male and female mouse ES cells were transfected with a mixture of three small interfering RNA duplexes, each of which targets a different region of Mof mRNA. We found that MOF knockdown in mouse ES cells caused a greater drop in expression of X-linked genes compared to autosomal genes, as measured by expression array analyses. The strongest effect was observed on medium-expressed X-linked genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

27 Samples

Download data: CEL

(Submitter supplied) Affymetrix 430 2.0 mouse arrays were used for expression analyses in undifferentiated and differentiated PGK12.1 ES cells. We found that the X:autosome expression ratios calculated from the mean expression values of X-linked and autosomal genes from microarrays was ~1.4 in undifferentiated female ES cells and then decreased to 1.2 in PGK12.1 cells after 15-day embryoid body differentiation. Thus, a substantial level of X upregulation is already evident in these ES cells prior to differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

2 Samples

Download data: CEL

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

Organism:

Mus musculus; Mus musculus x Mus spretus

Type:

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

9 related Platforms

60 Samples

Download data: BED, BIGWIG, CEL, GFF, PAIR, TXT

(Submitter supplied) Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9185

1 Sample

Download data: TXT

(Submitter supplied) Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9833

2 Samples

Download data: GFF, PAIR

(Submitter supplied) During interphase, the inactive X chromosome (Xi) adopts an unusual 3D configuration known as the Barr body and is largely transcriptionally silent. Despite the importance of X inactivation, little is known about the 3D configuration of Xi and its relationship to gene silencing. We recently showed that in humans, Xi exhibits two distinctive structural features. First, Xi is partitioned into two huge intervals, called superdomains, such that pairs of loci in each superdomain show an enhanced contact frequency with one another. more...

Organism:

Macaca mulatta; Homo sapiens; Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

5 related Platforms

101 Samples

Download data: HIC, PDF, TSV, TXT

(Submitter supplied) X-chromosome inactivation (XCI) entails a massive structural reorganization of the inactive X (Xi). However the molecular architecture of the Xi is unknown. Here we show that the Xi lacks typical autosomal features such as active/inactive compartments and topologically associating domains (TADs), except around a small number of genes that escape XCI and remain expressed. Escaping genes form TADs and retain DNA accessibility at promoter-proximal and CTCF binding sites, indicating that these loci can avoid Xist-mediated erasure of chromosomal structure. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other; Third-party reanalysis

Platform:

GPL13112

8 Samples

Download data: TAR, TXT