GEO DataSets

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

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(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

(Submitter supplied) Whole brain gene expression was examined in the following strains of mice: 1. P0 maternal monosomic 39,Xm females, C57BL/6J x C3H/Paf 2. P0 paternal monosomic 39, Xp females, In(X)/C3H x C57BL/6J 3. P0 normal 40,XX females, In(X)/C3H x C57BL/6J 4. P0 normal 40,XX females, C57BL/6J x C3H/Paf Keywords = imprinting Keywords = mammalian genetics Keywords = X-linked Keywords = brain Keywords: other

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1513

Platform:

GPL81

10 Samples

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Analysis of neonatal brains of X-monosomic females that inherited either a maternal or a paternal X chromosome. X-monosomy is the basis of Turner's syndrome (TS). Expressivity of TS phenotypes depends partly on the parental origin of the single X. This expressivity may be due to imprinted X genes.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 3 genotype/variation, 2 protocol sets

Platform:

GPL81

Series:

GSE1606

10 Samples

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(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) 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) 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) Heart deformity is the leading cause of mortality in Turner syndrome (TS) patients. To investigate the dysregulated ceRNA network in cardiomyocytes (CMs) of TS patients, we employed a ceRNA microarray to profile the mRNA-lncRNA-circRNA network in induced pluripotent stem cells (iPSCs) and their derived CMs from healthy donors (WT) and TS patients.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL22120

12 Samples

Download data: TXT

(Submitter supplied) Purpose: To understand how sex chromosome complement, XX, XO and XY, influences the transcriptome in the oocytes of grwoth phase. Methods: Oocytes of 50 and 60 µm in diameter were isolated from mouse ovaries at 18 dpp and subject to RNA-sequencing. Results: (1) Many X-linked genes are subject to X chromosome dosage dependent expression. (2) Many genes are expressed from both short and long arms of the Y chromosome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: BW, CSV

(Submitter supplied) Sexual dimorphism in mammals is mostly attributable to sex-related hormonal differences in fetal and adult tissues; however, this may not be the sole determinant. Though genetically-identical for autosomal chromosomes, male and female preimplantation embryos could display sex-specific transcriptional regulation which can only be attributted to the differences in sexual chromosome dosage. We used microarrays to analyze sex-related transcriptional differences at the blastocyst stage.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL2112

18 Samples

Download data: CEL

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

47 Samples

Download data: CSV

(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:

GPL19057 GPL21103

727 Samples

Download data

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

672 Samples

Download data: CSV, LOOM, XLSX

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: CSV

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) X-chromosome inactivation (XCI) achieves dosage compensation between males and females through the silencing of the majority of genes on one X chromosome, with approximately 15% of genes reported to show inactive X (Xi) expression. We examined the interplay between ChromHMM states, CpG density, expression and DNAm from over 1800 female samples with the Illumina 450K array. The interaction between CpG density and histone marks differed between the active X (Xa) and the Xi, with X-linked promoters reflecting transcriptional status, while the Xi showed lower DNAm than the Xa at all non-promoter regions. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

927 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) 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) To investigate the evolutionary divergence of transcriptional regulation between the mouse subspecies, we performed transcriptome analysis by microarray on testes from the X-chromosome substitution strain, which carries different subspecies-derived X chromosome on the host subspecies genome. Transcription profiling showed that large-scale aberrations in gene expression were occurred on the introgressed X chromosome. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

38 Samples

Download data: CEL, CHP

(Submitter supplied) Background: Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date a total of 255 imprinted genes have been identified or predicted among all investigated mammal species. However, only 21 have been described in sheep and 11 are annotated in current ovine genome. Results: Here we aim to use DNA/RNA throughput sequencing to identify monoallelically expressed and imprinted genes in organs of day 135 fetal sheep, and 2) to determine whether different levels of maternal energy intake (100% of NRC energy requirement or control, 140% or over-, and 60% or under-fed) influence genomic imprinting. more...

Organism:

Ovis aries

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL22509 GPL15670

49 Samples

Download data: TXT