(methylation profiling by array[DataSet Type] OR methylation profiling - GEO DataSets

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Select item 2002273251.

Pre-weaning heat stress alters liver DNA methylation in dairy calves

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

Organism:: Bos taurus

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

Platforms:: GPL23295 GPL26012
23 Samples

Download data

Series

Accession:: GSE227325

ID:: 200227325

Select item 2002272492.

Pre-weaning heat stress alters liver DNA methylation in dairy calves [Bisulfite-Seq]

(Submitter supplied) The impact of postnatal heat stress exposure in neonatal calves is not well-understood, and adequate heat abatement methods during the pre-weaning phase are lacking. This study aimed to investigate the impact of pre-weaning heat stress on liver DNA methylation profiles.

Organism:: Bos taurus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL23295
11 Samples

Download data

Series

Accession:: GSE227249

ID:: 200227249

Select item 2002274883.

Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity

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

Organism:: Homo sapiens; unidentified

Type:: Methylation profiling by genome tiling array; Expression profiling by array

Platforms:: GPL13534 GPL6884 GPL21145
135 Samples

Download data: IDAT, TXT

Series

Accession:: GSE227488

ID:: 200227488

Analyze with GEO2R

Select item 2002274854.

Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity [humanmethylation450]

(Submitter supplied) Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related Th cells (type 17 cells) and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cells in vivo. By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing RORt. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
24 Samples

Download data: IDAT, TXT

Series

Accession:: GSE227485

ID:: 200227485

Analyze with GEO2R

Select item 2002274845.

Human CCR6+ Th cells show both an extended stable gradient of Th17 activity and imprinted plasticity [methylationEPIC]

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL21145
30 Samples

Download data: IDAT, TXT

Series

Accession:: GSE227484

ID:: 200227484

Analyze with GEO2R

Select item 2002234806.

A hyper-quiescent chromatin state formed during aging is reversed by regeneration

(Submitter supplied) Epigenetic alterations are a key hallmark of aging but have not been extensively explored in tissues. Here, using naturally aged murine liver as a model and extending study to other quiescent tissues, we find that aging is driven by temporal chromatin alterations that promote a refractory cellular state and compromise cellular identity. Using an integrated multi-omics approach and the first direct visualization of aged chromatin, we find that old cells show global H3K27me3-driven broad heterochromatinization and transcription suppression. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL30172
16 Samples

Download data: BW

Series

Accession:: GSE223480

ID:: 200223480

Select item 2002162067.

Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys

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

Organism:: Homo sapiens; Macaca fascicularis

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

4 related Platforms
47 Samples

Download data: MTX, TSV, TXT

Series

Accession:: GSE216206

ID:: 200216206

Select item 2002162028.

Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys (EM-Seq)

(Submitter supplied) Human in vitro oogenesis provides a framework for clarifying the mechanism of human oogenesis. To create its benchmark, it is vital to promote in vitro oogenesis using a model physiologically close to humans. Here, we establish a foundation for in vitro oogenesis in cynomolgus (cy) monkeys (Macaca fascicularis): cy female embryonic stem cells harboring one active and one inactive X chromosome (Xa and Xi, respectively) differentiate robustly into primordial germ cell-like cells, which in xenogeneic reconstituted ovaries develop efficiently into oogonia and, remarkably, further into meiotic oocytes at the zygotene stage. more...

Organism:: Macaca fascicularis; Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platforms:: GPL24676 GPL28212
13 Samples

Download data: TXT

Series

Accession:: GSE216202

ID:: 200216202

Select item 2001989109.

hMeDIP-Seq of Tet2 overexpressing hippocampal neurons

(Submitter supplied) Tet2 regulates gene expression by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine. Profiling the genomic locations of 5-hydroxymethylcytosine after Tet2 manipulation can inform us of the targets of Tet2 regulation. We profiled hydroxymethylcytosine in Tet2 ovexpressing neurons to determine the targets of Tet2 in neurons.

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL21103
11 Samples

Download data: TXT

Series

Accession:: GSE198910

ID:: 200198910

Select item 20018570810.

A hyper-quiescent chromatin state is a barrier to productive regeneration during aging.

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

Organism:: Mus musculus; Homo sapiens

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

4 related Platforms
256 Samples

Download data: BW, TXT

Series

Accession:: GSE185708

ID:: 200185708

Analyze with GEO2R

Select item 20018059711.

HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [Methyl-seq]

(Submitter supplied) Recent advances in synthetic mammalian embryo models have opened new avenues to understand the complex events controlling lineage decisions and morphogenetic processes occurring during peri-implantation and early organogenesis. Two main strategies have been developed to build embryo-like structures (ELS): by assembling extraembryonic and embryonic stem cells (ESCs) or by subjecting ESCs to various morphogens. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL21103
15 Samples

Download data: BED

Series

Accession:: GSE180597

ID:: 200180597

SRA Run Selector

Select item 20018048912.

HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure

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

Organism:: Mus musculus

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

Platforms:: GPL19057 GPL21103
289 Samples

Download data: BED, BW

Series

Accession:: GSE180489

ID:: 200180489

Select item 20019988513.

Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration

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

Organism:: Mus musculus

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

Platform:: GPL24247
62 Samples

Download data: BW, MTX, TSV

Series

Accession:: GSE199885

ID:: 200199885

Select item 20019988314.

Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration [WGBS]

(Submitter supplied) De novo germline histone H3.3 amino acid substitutions, including H3.3G34R/V, cause severe neurodevelopmental syndromes. To understand how these mutations impact brain development, we generated heterozygous H3.3G34R/V/W direct knock-in mutant mice and identified strikingly distinct developmental defects for each amino acid substitution. H3.3G34R-mutant mice uniquely exhibited progressive microcephaly and neurodegeneration, associated with abnormal accumulation of damage-associated microglia and astrocytes, and concurrent neuronal depletion in postnatal brains. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL24247
4 Samples

Download data: BW

Series

Accession:: GSE199883

ID:: 200199883

Select item 20019869315.

Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development

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

Organism:: Physcomitrium patens

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

Platforms:: GPL30955 GPL29161 GPL30513
8 Samples

Download data: GFF

Series

Accession:: GSE198693

ID:: 200198693

Select item 20019759216.

Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [Bisulfite-seq]

(Submitter supplied) We mutated PpDDM1 and the early land plant. Using BS-seq and RNA-seq, we here show that though DNA methylation is disrupted in all contexts development isn't and TE and gene differential expression are minute

Organism:: Physcomitrium patens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL29161
2 Samples

Download data: GFF

Series

Accession:: GSE197592

ID:: 200197592

Select item 20022656017.

Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [Bisulfite-seq]

(Submitter supplied) Background Long non-coding RNAs (lncRNAs) are under-studied and under-annotated in plants. In mammals, lncRNA expression has been shown to be reaching the extent of protein-coding expression and be highly variable between individuals of the same species. Using A. thaliana as a model plant organism, we aimed to understand the true scope of lncRNA transcription across plants from different regions, characterize lncRNA natural expression variability, and study the causes of this variability. more...

Organism:: Arabidopsis thaliana

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL26208
88 Samples

Download data: TXT

Series

Accession:: GSE226560

ID:: 200226560

Select item 20022476118.

Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing

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

Organism:: Arabidopsis thaliana

Type:: Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL24270 GPL17639 GPL26208
453 Samples

Download data

Series

Accession:: GSE224761

ID:: 200224761

Select item 20021400619.

Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine

(Submitter supplied) Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5fC) utilizing 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT+ BF4–) and further transformation of 5fC into 5-carboxycytosine (5caC) through Pinnick oxidation. more...