GEO DataSets

(Submitter supplied) Disappearance of the Barr body has long been considered a hallmark of cancer, although whether this corresponds to epigenetic instability and transcriptional reactivation, or to genetic loss, has remained unclear. Here we show that in breast cancer cell lines as well as primary breast tumors, the inactive X chromosome frequently displays a highly abnormal 3D nuclear organization, with global perturbations in its characteristic heterochromatic state, including apparent gain of euchromatic marks and lessening of repressive marks such as H3K27me3 and promoter DNA methylation. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL16791

29 Samples

Download data: BEDGRAPH, FPKM_TRACKING, TXT, XLS

(Submitter supplied) Disappearance of the Barr body has long been considered a hallmark of cancer, although whether this corresponds to epigenetic instability and transcriptional reactivation, or to genetic loss, has remained unclear. Here we show that in breast cancer cell lines as well as primary breast tumors, the inactive X chromosome frequently displays a highly abnormal 3D nuclear organization, with global perturbations in its characteristic heterochromatic state, including apparent gain of euchromatic marks and lessening of repressive marks such as H3K27me3 and promoter DNA methylation. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

10 Samples

Download data: CEL, TXT

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

Platforms:

GPL11154 GPL16791 GPL6801

39 Samples

Download data: BEDGRAPH, CEL, FPKM_TRACKING, 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; Mus musculus x Mus spretus

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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus x Mus spretus; Mus musculus

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) Comparison of H3K9me3 and H3K27me3 distribution in homogeneous XaXi and XaXe H9 human embryonic stem cells and in IMR90 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: BED

(Submitter supplied) Erasure of epigenetic memory is required to convert somatic cells towards pluripotency. Reactivation of the inactive X chromosome (Xi) has been used to model epigenetic reprogramming in mouse, but human studies are hampered by Xi epigenetic instability and difficulties in tracking partially reprogrammed iPSCs. Here we used cell fusion to examine the earliest events in the reprogramming-induced Xi reactivation of human female fibroblasts. more...

Organism:

Homo sapiens; Homo sapiens x Mus musculus hybrid cell line

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19068 GPL16791

4 Samples

Download data: TXT

(Submitter supplied) We performed RNA-seq experiments to modulate levels of XIST RNA. We inhibited XIST activity in REH lymphocytic cells via knockdown of XIST expression by short hairpin (sh) RNA. We confirmed that the RNA level of XIST was greatly reduced in shRNA-XIST cells by both RNA-seq and qPCR analyses, relative to cells transfected with a scrambled shRNA.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: TXT

(Submitter supplied) This study concerns the dynamics of reprogramming of the inactive X chromosome in the inner cell mass of the E3.5-4.5 mouse blastocysts. We use single cell, allele-specific transcriptomic analyses to define the precise timing of paternal X-linked gene reactivation, as well as nascent RNA FISH and immunuofluorescence to follow the loss of chromatin marks such as H3K27me3. We find evidence that different genes show very different timing of reactivation indicating an epigenetic memory of the inactive state in some cases but not in others. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

40 Samples

Download data: XLS

(Submitter supplied) We examined genome-wide, base-resolution, allele-specific methylation and expression in the prefrontal cortex using a mouse model of deterministic X-inactivation, where the paternal allele was always inactivated. Our findings elucidate the role methylation may play in chromatin regulation under X-inactivation and genomic imprinting.

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

4 Samples

Download data: BW, TAR, TXT

(Submitter supplied) Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis and the derivation of induced pluripotent stem cells (iPSCs). X-chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. While XCI has long been studied and provided important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. more...

Organism:

Mus musculus musculus x Mus musculus castaneus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26166

7 Samples

Download data: XLS

(Submitter supplied) To investigate the dynamics of X-chromosome reactivation, we differentiated mouse embryonic stem cells (ESCs) into neural precursor cells (NPCs) and later reprogrammed them into induced pluripotent stem cells (iPSCs). During the conversions of NPCs into iPSC, we assessed the kinetics of X-chromosome reactivation. We generated allele-specific RNA-seq datasets to assess gene reactivation dynamics, employed ATAC-seq to investigate chromatin opening dynamics and performed in situ Hi-C to explore dynamics of chromosome structure.

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

116 Samples

Download data

(Submitter supplied) X chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell. In order to characterize epigenetic changes that accompany this process, we measured DNA methylation levels in both 45,X Turner syndrome patients, who carry a single active X chromosome (Xa) and normal 46,XX females, who carry one Xa and one inactive X (Xi). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL10573

23 Samples

Download data: PAIR

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL18480 GPL11002

8 Samples

Download data