GEO DataSets

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

Type:

Expression profiling by high throughput sequencing

4 related Platforms

15 Samples

Download data: TXT

(Submitter supplied) The discovery of genomic imprinting through studies of manipulated mouse embryos indicated that the paternal genome has a major influence on placental development. However, previous research has not demonstrated paternal bias in imprinted genes. We applied RNA sequencing to trophoblast tissue from reciprocal hybrids of horse and donkey, where genotypic differences allowed parent-of-origin identification of most expressed genes. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: SAM

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

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array; Expression profiling by high throughput sequencing

Platforms:

GPL16288 GPL18544

40 Samples

Download data

(Submitter supplied) Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18544

30 Samples

Download data: TXT

(Submitter supplied) Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16288

10 Samples

Download data: TXT

(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) 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) 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) Evolution of the mammalian sex chromosomes has resulted in a heterologous X and Y pair, where the Y chromosome has lost most of its genes. Hence, there is a need for X-linked gene dosage compensation between XY males and XX females. In placental mammals, this is achieved by random inactivation of one X chromosome (XCI) in all female somatic cells. Up-regulation of Xist transcription on the future inactive X chromosome (Xi) acts against Tsix antisense transcription, and spreading of Xist RNA in cis triggers epigenetic changes leading to XCI. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: BEDGRAPH

(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) Mammals have evolved a mechanism to compensate for the difference in the number of X chromosome genes between XX females and XY males by inactivating one of the two X chromosomes in females. This X chromosome inactivation phenomenon is triggered by Xist gene, which is essential for X-inactivation to occur in cis. We demonstrate that an Xist mutant, XistIVS, is unique in that it retains a partial function to silence the X chromosome, which would provide an opportunity to dissect the molecular mechanism of Xist RNA-mediated chromosome silencing.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13133

4 Samples

Download data: TXT

(Submitter supplied) Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on E17.5 mouse placenta cDNA samples from reciprocal cross F1 progeny of AKR and PWD mouse strains, and quantified the allele-specific expression and the degree of parent-of-origin effect transcriptome-wide. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9185

2 Samples

Download data: SAM

(Submitter supplied) Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 genes have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ~105 Bos taurus indicus X Bos taurus taurus F1 conceptuses using RNA sequencing. more...

Organism:

Bos indicus; Bos indicus x Bos taurus

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platforms:

GPL21383 GPL20723

5 Samples

Download data: VCF, XLSX

(Submitter supplied) Maternal imprinting at the Xist gene is essential to achieve paternal allele-specific imprinted X chromosome inactivation (XCI) in female mammals. However, the mechanism underlying the Xist imprinting is unclear. Here we show that the Xist gene is coated with H3K27me3 in mouse oocytes, which persists through preimplantation development. Ectopic removal of H3K27me3 induces maternal Xist expression and maternal XCI, indicating that maternal H3K27me3 is the imprinting mark of Xist.

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

8 Samples

Download data: BED, XLSX

(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) 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

Platform:

GPL18573

23 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) We analysed by Reduced Representation Bisulfite Sequencing (RRBS) the genome methylation pattern in human fibroblast and in naïve induced pluripoent stem cells (niPSCs)

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA-seq based transcriptome analysis of human fibroblast, primed and naïve induced pluripoent stem cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

13 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

32 Samples

Download data: CSV, TXT

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

Organism:

Mus musculus; Macaca fascicularis

Type:

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

Platforms:

GPL18648 GPL13112

71 Samples

Download data