GEO DataSets

(Submitter supplied) The spatial proximity between regulatory elements and their target genes has a profound affect on gene expression. X Chromosome Inactivation (XCI) is an epigenetic process by which an entire chromosome is rendered, for the most part, transcriptionally silent. A few genes are known to escape XCI and the mechanism for this escape remains unclear. Here, using mouse trophectodermal stem cells, we address whether specific chromosomal interactions facilitate escape from XCI by bringing escape-specific regulatory elements in close proximity to gene promoters. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells containing a single X chromosome. We use mouse female Embryonic Stem Cells (ESCs) with nonrandom XCI and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome (Xi) by high-resolution allele-specific RNA-Seq. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL11002 GPL19057

20 Samples

Download data: BED, TXT, WIG

(Submitter supplied) In this study, we explored x-inactivation in monkey embryos (ICM and TE separately) and pluripotent stem cells (IVF derived ES, SCNT-derived ES and monkey iPS) To elucidate x-inactivation in experimentally reprogrammed pluripotent cells, we derived pluripotent stem cells by both SCNT and iPS approaches from same parental skin fibroblasts. We also compared gene patterns of those cells to IVF-derived counterpart.

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL3535

21 Samples

Download data: CEL, CHP

(Submitter supplied) Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which characterizes many silenced genes including those on the inactive X-chromosome. Here we interrogate the role of core PRC2 protein EED in X-linked gene silencing by assessing allele-specific X-linked gene expression in WT and Eed-/- hybrid mouse trophoblast stem cells (TSCs) harboring a 129/S1-derived maternal X-chromosome and a JF1/Ms-derived paternal X-chromosome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: BEDGRAPH, TXT

(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) 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) 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) In order to test the hypothesis that X chromosome inactivation shows sequence specificity, we have analysed the spread of XCI into autosomal chromatin by performing DNA methylation profiling in six unbalanced X;autosome translocations. Using promoter hypermethylation as an epigenetic signature of XCI, we have determined the inactivation status of 1,050 autosomal genes after translocation onto the inactive X. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

8 Samples

Download data: TXT

(Submitter supplied) We report the application of Chromosome Conformation Capture Carbon-copy (5C) to a 4.5 Mb stretch of the mouse X chromosome encompassing the X inactivation center locus. We uncover a series of discrete 200kb-1Mb topologically associating domains (TADs). These align with several domain-wide epigenomic features as well as co-regulated gene clusters. 5C analysis in EED and G9A mutants reveal that this segmental organisation in TADs does not relie on the underlying H3K27me3 or H3K9me2 blocks. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL11002

20 Samples

Download data: FA, TXT

(Submitter supplied) Embryonic stem cells (ESC) are derived from the inner cell mass of the blastocyst in the presence of leukemia inhibitory factor (LIF). In vivo these cells then differentiate into epi stem cells (EpiSC) that can be derived from the Epiblast in presence of Fgf2 and ActivinA. In this study, female ESCs cultured in 2i medium have been differentiated into EpiSC for 3.5 days in vitro by addition of Fgf2 and Activin A. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6193

17 Samples

Download data: CEL

(Submitter supplied) X-chromosome inactivation (XCI) provides a dosage compensation mechanism where, in each female cell, one of the two X chromosomes is randomly silenced. However, some genes on the inactive X chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). We investigated XCI at single-cell resolution combining deep single cellRNA sequencing with whole-genome sequencing to examine allelic-specific expression in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

820 Samples

Download data: CSV

(Submitter supplied) Skewed X-chromosome inactivation (XCI) plays an important role in the phenotypic heterogeneity of X-linked disorders. However, the role of skewed XCI in XCI–escaping gene SHOX regulation is unclear. Here, we focused on a heterozygous deletion of SHOX gene enhancer with clinical heterogeneity. Using SNP array, we detected that the female proband with Leri-Weill dyschondrosteosis (LWD) carried an 857 kb deletion on Xp22.3 (encompassing SHOX enhancer) and a 5,707 kb large-fragment deletion on Xq25q26. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

3 Samples

Download data: CEL, CYCHP

(Submitter supplied) Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. more...

Organism:

Monodelphis domestica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15381

16 Samples

Download data: TXT

(Submitter supplied) Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. more...

Organism:

Monodelphis domestica

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15381

8 Samples

Download data: BED

(Submitter supplied) X chromosome inactivation (XCI) is a dosage compensation mechanism in female cells to regulate X-linked gene expression. We report here that subcultures from established lines of female hESCs displayed variations (0-100%) in the expression of XCI markers such as XIST RNA coating and enrichment of histone H3 lysine 27 trimethylation (H3K27me3) on inactive X chromosome. Surprisingly, regardless of the presence or absence of XCI markers in different cultures, all female hESCs we examined (H7, H9, and HSF6 cells) exhibit a mono-allelic expression pattern for a majority of X-linked genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array; Methylation profiling by genome tiling array; SNP genotyping by SNP array

4 related Platforms

9 Samples

Download data: CEL, CHP, TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL9185 GPL8656

58 Samples

Download data: BED, GFF, TXT, WIG

(Submitter supplied) This study describes the epigenetic profiling of the X chromosome during X inactivation. It includes H3K4me3 and H3K27me3 ChIP-Seq profiles of male (E14) and female (LF2 and XT67E1) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB). It also includes ChIP-chip profiles around the Xic on chromosome X of H3K4me3, H3K27me3, H3K9me2, H3K36me3, Pol II, TBP, H3-Core as well as expression, using male (E14) and female (LF2) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array

Platform:

GPL8656

48 Samples

Download data: GFF, TXT

(Submitter supplied) This study describes the epigenetic profiling of the X chromosome during X inactivation. It includes H3K4me3 and H3K27me3 ChIP-Seq profiles of male (E14) and female (LF2 and XT67E1) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB). It also includes ChIP-chip profiles around the Xic on chromosome X of H3K4me3, H3K27me3, H3K9me2, H3K36me3, Pol II, TBP, H3-Core as well as expression, using male (E14) and female (LF2) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

10 Samples

Download data: BED, WIG

(Submitter supplied) Genomic imprinting is essential for mammalian development. Recent studies have revealed that maternal histone H3 lysine 27 tri-methylation (H3K27me3) can mediate DNA methylation-independent genomic imprinting. However, the regulatory mechanisms and functions of this new imprinting mechanism are largely unknown. Here we demonstrate that maternal Eed, an essential component of the Polycomb group complex 2 (PRC2), is required for establishing H3K27me3 imprinting. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

19 Samples

Download data: BW, XLSX