GEO DataSets

(Submitter supplied) The H3K27me3 is a repressive histone mark associated with repressive chromatin and is important for X chromosome inactivation. ChIP-chip of H3K27me3 along the mouse X chromosome in male and female livers and p12.5 embryos demonstrated that H3K27me3 is absent at the genes that escape X inactivation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10129

4 Samples

Download data: PAIR, TXT

(Submitter supplied) Gobal expression analysis in four somatic tissues (brain, liver, kidney and muscle) of adult 40,XX and 39,XO mice with the aim of identifying which genes are expressed from both X chromosomes as well as those genes deregulated in X chromosome monosomy. Keywords: Expression profiling by array

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3728

Platform:

GPL6105

36 Samples

Download data: TXT

Analysis of four somatic tissues (brain, liver, kidney and muscle) from 12-week-old 40,XX and X monosomic (39,XO) mice. In humans, complete or partial monosomy of the X chromosome results in Turner syndrome (45,XO). Genes deregulated in XO mice provide insight into the molecular basis of TS.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 3 genotype/variation, 4 tissue sets

Platform:

GPL6105

Series:

GSE13520

36 Samples

Download data

(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) To investigate the epigenetic landscape at the interface between mother and fetus, we provide a comprehensive analysis of parent of origin bias in the placenta. Using F1 interspecies hybrids, we sequenced RNA from 23 individual midgestation placentas, five late stage placentas, and two yolk sac samples and then used SNPs to determine whether transcripts were preferentially generated from the maternal or paternal allele. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

31 Samples

Download data: BED

(Submitter supplied) Cis-regulatory variants are predicted to mediate the majority of the common genetic risk associated to complex disease, yet the specific causal variants have thus far been poorly characterized. Allele-specific (AS) assessment of chromatin modifications has the potential to elucidate specific cis-regulatory mechanisms. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depth not commonly applied in next-generation sequencing based approaches. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

4 related Platforms

224 Samples

Download data: TXT

(Submitter supplied) Parent-of-origin dependent expression of alleles, imprinting, has been suggested to impact a substantial proportion of mammalian genes. Its discovery requires allele-specific detection of expressed transcripts, but in some cases detected allelic expression (AE) bias has been interpreted as imprinting without demonstrating compatible transmission patterns and excluding heritable variation. Therefore, we utilized a genome-wide tool exploiting high density genotyping arrays in parallel measurements of genotypes in RNA and DNA to determine AE across the transcriptome in lymphoblastoid cell lines (LCLs) and skin fibroblasts derived from families.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL6984 GPL6983

112 Samples

Download data

(Submitter supplied) This analysis includes H3K27me3 profiles along the length of the X-chromosome in male (F2) and female (K4) TS cells and in female TS cells showing local reversals of imprinted X-chromosome inactivation (K4GFP). Data also includes H3K27me3 ChIP-chip profiles in Eed-/- mutant male and female TS cells obtained from Magnuson laboratory (Kalantry S. et al., Nat Cell Biol, 2006).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14676

10 Samples

Download data: PAIR

(Submitter supplied) Background: In both Turner syndrome (TS) and Klinefelter syndrome (KS) copy number aberrations of the X chromosome lead to various developmental symptoms. To date there has not been a comprehensive and directly comparative analysis of TS vs. KS regarding the changes on the molecular level Methods: We analyzed gene expression patterns with RNA-Seq and DNA methylation patterns with the CpGiant assay in lymphocytes, and chromatin conformation with in situ Hi-C in lymphoblastoid cell lines, from TS and KS patients together with their same gender controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL18573 GPL20301

70 Samples

Download data: TSV, TXT

(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: 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:

GPL20213 GPL16616

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) 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:

GPL16733 GPL10129 GPL16143

25 Samples

Download data: PAIR