GEO DataSets

(Submitter supplied) Direct neuronal reprogramming is a promising approach to regenerate neurons from local glial cells. However, mechanisms of epigenome remodeling and co-factors facilitating this process are unclear. Here, we combine single-cell multiomics with genome-wide profiling of 3D nuclear architecture and DNA methylation in mouse astrocyte-to-neuron reprogramming mediated by Neurogenin2 (Ngn2) and its phosphorylation-resistant form (PmutNgn2), respectively. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL18480 GPL32159

64 Samples

Download data: BED, BEDGRAPH, BW, MTX, NARROWPEAK, TAB, TSV, TXT, XLSX

(Submitter supplied) Limb development is a well-established model for understanding cell fate decisions, and the formation of skeletal elements is coordinated through a sequence of events that control chondrogenesis spatiotemporally. It has been established that epigenetic control participates in cartilage maturation. Our research has shown for the first time that the inhibition of DNA methylation in interdigital tissue with 5-azacytidine results in the formation of an ectopic digit. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26853

4 Samples

Download data: TXT

(Submitter supplied) Isocitrate Dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores anti-tumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: COV

(Submitter supplied) Isocitrate Dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores anti-tumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: COV

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL24676 GPL24247 GPL18573

127 Samples

Download data: COV

(Submitter supplied) Isocitrate Dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores anti-tumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: COV

(Submitter supplied) Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of 12 different growing teratoma tissues. Samples were subgrouped based on growth speed into GTSslow to GTSrapid (see corresponding publication).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

12 Samples

Download data: IDAT

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

Organism:

Rattus norvegicus

Type:

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

Platforms:

GPL32190 GPL22396

13 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Background. Prenatal exposure to nicotine has been documented to impose numerous deleterious effects on fetal development. However, the epigenetic changes promoted by nicotine exposure on germ cell are still not well understood. Objectives. In this study, we focused on elucidating the impact of prenatal nicotine exposure on regulatory epigenetic mechanisms important for the germ cells development. s important for the germ cells development

Organism:

Rattus norvegicus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL32190

7 Samples

Download data: BEDGRAPH

(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; Methylation profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

66 Samples

Download data: BW, TXT

(Submitter supplied) Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type and mutant MECP2 molecules. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676

123 Samples

Download data: BW, TXT

(Submitter supplied) XIST long non-coding RNA is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female pre-implantation embryos without triggering X chromosome silencing. The long non-coding RNA XACT co-accumulates with XIST on active Xs and may antagonize XIST function. Here we used human ES cells in a naïve state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during pre-implantation development. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TXT

(Submitter supplied) The participants performed 8 weeks of superised aerobic endurance exercise. Skeletal muscle biopsise were taken at rest before and after intervention and matched analysis was performed.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

36 Samples

Download data: IDAT

(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:

GPL24676 GPL18573

119 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Epigenetic reprogramming resets parental epigenetic memories and differentiates primordial germ cells (PGCs) into mitotic pro-spermatogonia or oogonia, ensuring sexually dimorphic germ-cell development for totipotency. However, the mechanism of epigenetic reprogramming in humans remains unknown. Here, we establish a robust strategy for inducing epigenetic reprogramming and differentiation of pluripotent stem cell (PSC)-derived human PGC-like cells (hPGCLCs) into mitotic pro-spermatogonia or oogonia, coupled with their extensive amplification (~>10(10)-fold). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

23 Samples

Download data: TXT

(Submitter supplied) This study characterized variations in the methylation profile of mitochondrial DNA (mtDNA) during initial bovine embryo development and correlated the presence of methylation with mtDNA transcription. Bovine oocytes were obtained from abattoir ovaries and submitted to in vitro culture procedures. Oocytes and embryos were collected at various stages (immature oocyte, IM; mature oocyte, MII; zygote, ZY; 4-cells, 4C; 16-cells, 16C and blastocysts, BL). more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26012

18 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL31191 GPL24247

158 Samples

Download data: IDAT

(Submitter supplied) Trophectoderm biopsy for preimplantation genetic testing (TEBx) impacts placental and embryonic health during early development, with some alterations resolving while others worsening later in development. We observed that at E12.5, IVF + TEBx had a worse outcome in terms of changes in DNA methylation and differential gene expression in placentas and whole embryos compared with IVF alone. These changes were reflected in alterations in placental morphology and blood vessel density. more...

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL31191

48 Samples

Download data: IDAT, XLSX

(Submitter supplied) Genome wide DNA methylation profiling of samples with/without chronic or acute Temporomandibular Disorders (TMD). The Illumina Infinium Human methylationEPIC Beadchip was used to obtain DNA methylation profiles across 1,051,943 CpGs in TMD samples. Samples included 452 non-TMD and 496 chronic TMD from OPPERA I, 36 healthy and 123 acute TMD from OPPERA II.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

1107 Samples

Download data: CSV, IDAT