GEO DataSets

(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) X chromosome inactivation (XCI) is critical for the development of the extraembryonic tissue as well as the embryonic tissue. Here we carried out transcriptomic analysis of the trophoblast isolated from two different Xist mutant embyros at E7.5 in comparison with wild-type.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

16 Samples

Download data: TXT

(Submitter supplied) Comparison of mouse ES cells and three different XEN cell cultures. Three XEN cell cultures: Two different strains (IM8A1 is PO, and XEN1-3 is ICR). And two different culture conditions (IM8A1-I versus IM8A1-II). Three biological replicates of XEN cell RNA were submitted to the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada) for preparation of cRNA and hybridization to the mouse U74Av2 Affymetrix gene array. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1763

Platform:

GPL81

4 Samples

Download data: CEL, EXP, RPT

Analysis of blastocyst-derived extra-embryonic endoderm (XEN) cell lines and an embryonic stem (ES) cell line. Results identify independent XEN cell lines that express markers of extra-embryonic endoderm, but not those of the epiblast, and thus represent a new model of an early mammalian lineage.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 cell line, 2 cell type, 3 growth protocol, 3 strain sets

Platform:

GPL81

Series:

GSE2204

4 Samples

Download data: CEL, EXP, RPT

(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) 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 analysis includes H3K27me3 profiles along the length of the X-chromosome in male (F2) and female (F3) TS cells and in female TS cells showing a complete reversal of X-chromosome inactivation (F3 clone1#A).

Organism:

Mus musculus

Type:

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

Platform:

GPL14676

6 Samples

Download data: PAIR

(Submitter supplied) In eutherian mammals, dosage compensation of X-linked genes is achieved by X chromosome inactivation. X inactivation is random in embryonic and adult tissues, but imprinted X inactivation (paternal X silencing) has been identified in the extraembryonic membranes of the mouse, rat, and cow. Few other species have been studied for this trait, and the data from studies of the human placenta have been discordant or inconclusive. more...

Organism:

Equus asinus; Equus asinus x Equus caballus; Equus caballus; Equus caballus x Equus asinus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

15 Samples

Download data: TXT

(Submitter supplied) Dosage compensation in mammals involves silencing of one X chromosome in XX females, and requires expression, in cis, of Xist silencing RNA. Using microarray analysis to assay expression of X-linked genes in mouse embryonic stem cells, we show that dosage compensation also involves global up-regulation of expression from the active X in both males and females. Up-regulation is complete (ie. 2-fold) only after 2-3 weeks of differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL5638

24 Samples

Download data: GPR

(Submitter supplied) X-chromosome dosage compensation ensures balanced gene dosage between the X chromosome and autosomes and between the sexes, involving divergent mechanisms among mammals. We elucidated a distinct mechanism for X-chromosome inactivation (XCI) in cynomolgus monkeys, a model for human development. The trophectoderm and cytotrophoblast acquire XCI around implantation through an active intermediate bearing repressive modifications and compacted structure, whereas the amnion, epiblast, and hypoblast maintain such an intermediate protractedly, attaining XCI by a week after implantation. more...

Organism:

Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27448 GPL22523 GPL19944

195 Samples

Download data: TXT

(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

(Submitter supplied) It has been shown that functional deficiency of SmcHD1, a noncanonical member of SMC family proteins, results in derepression of X-inactivated genes in postimplantation female mouse embryos. In this study, we found that derepression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

4 Samples

Download data: TXT

(Submitter supplied) It has been shown that functional deficiency of SmcHD1, a noncanonical member of SMC family proteins, results in derepression of X-inactivated genes in postimplantation female mouse embryos. In this study, we found that derepression of X-inactivated genes accompanied a local reduction in the enrichment of H3K27me3 in mouse embryonic fibroblasts (MEFs) prepared from female fetuses deficient for SmcHD1.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

4 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676

38 Samples

Download data: TXT

(Submitter supplied) Human embryonic stem cells (hESCs) readily differentiate to somatic or germ lineages but have impaired ability to form extra-embryonic lineages such as placenta or yolk sac. Here we demonstrate that hESCs cultured in naïve media conditions can be converted into cells that exhibit the cellular and molecular phenotypes of human trophoblast stem cells (hTSCs) derived from human placenta or blastocyst. The resulting “transdifferentiated” hTSCs show reactivation of core placental genes, acquisition of a placenta-like methylome, and the ability to differentiate to extravillous trophoblasts and syncytiotrophoblasts. Modest differences are observed between transdifferentiated and placental hTSCs, most notably in the expression of certain imprinted loci. These results indicate that naïve hESCs can differentiate to extra-embryonic lineage, and demonstrate a new way of modeling human trophoblast specification and placental methylome establishment.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

33 Samples

Download data: TXT

(Submitter supplied) Human embryonic stem cells (hESCs) readily differentiate to somatic or germ lineages but have impaired ability to form extra-embryonic lineages such as placenta or yolk sac. Here we demonstrate that hESCs cultured in naïve media conditions can be converted into cells that exhibit the cellular and molecular phenotypes of human trophoblast stem cells (hTSCs) derived from human placenta or blastocyst. The resulting “transdifferentiated” hTSCs show reactivation of core placental genes, acquisition of a placenta-like methylome, and the ability to differentiate to extravillous trophoblasts and syncytiotrophoblasts. Modest differences are observed between transdifferentiated and placental hTSCs, most notably in the expression of certain imprinted loci. These results indicate that naïve hESCs can differentiate to extra-embryonic lineage, and demonstrate a new way of modeling human trophoblast specification and placental methylome establishment.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

5 Samples

Download data: TXT

(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