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Items: 1 to 20 of 10227

1.

Mechanism of initial favourable response to decitabine in TP53 mutated MDS/AML and potential mechanisms of subsequent relapses

(Submitter supplied) Myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) with complex and monosomy karyotype (CK/MK) show high prevalence of TP53 mutations, poor response to induction chemotherapy and adverse patient outcome. These diseases may respond to decitabine but the mechanisms are presently unclear. MDS/AML patients were treated with decitabine for 10 days in a Phase II clinical study. In this study, we collected serial samples from patients before and at completion of decitabine treatment, morphologic remission and relapse. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24106
36 Samples
Download data: CSV
Series
Accession:
GSE279925
ID:
200279925
2.

Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells.

(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:
GPL21103 GPL17021 GPL24247
96 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE267053
ID:
200267053
3.

Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells [EM-seq]

(Submitter supplied) Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it remains uncertain whether disordered epigenetic mechanisms can be fully corrected. Disruption of DNA methyltransferase 1 (DNMT1), responsible for DNA methylation maintenance, has particularly devastating biological consequences. Therefore, here we explored if rescuing DNMT1 activity is sufficient to reverse the effects of its loss utilizing mouse embryonic stem cells. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24247
9 Samples
Download data: BED, TXT
Series
Accession:
GSE266926
ID:
200266926
4.

Transcriptome-wide characterization of m6A methylation in colorectal cancer

(Submitter supplied) N6-Methyladenosine (m6A) is the most prevalent internal chemical modification of mRNAs in eukaryotes, and m6A methylations are crucial in cancer development. We characterized RNA m6A methylation in colorectal cancer to investigate its association with current molecular phenotyping system.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24676
24 Samples
Download data: XLSX
Series
Accession:
GSE196429
ID:
200196429
5.

A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State

(Submitter supplied) The distinct states of pluripotency in the pre- and post-implantation embryo can be captured in vitro as naive and primed pluripotent stem cell cultures, respectively. The study and application of the naive state remains hampered, particularly in humans, partially due to current culture protocols relying on extraneous undefined factors such as feeders. Here we performed a small-molecule screen to identify compounds that facilitate chemically defined establishment and maintenance of human feeder-independent naive embryonic (FINE) stem cells. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL21145
6 Samples
Download data: XLSX
Series
Accession:
GSE288982
ID:
200288982
6.

Comprehensive Analysis of DNA Methylation Patterns in Recurrent Miscarriage: Imprinted Genes and Their Regulation Across Sperm and Fetal-Maternal Tissues

(Submitter supplied) Genome-wide DNA methylation profiling was performed on sperm (n=3) and chorionic villi (n=3) from RM patients and control couples undergoing artificial abortion using the Illumina HumanMethylation 450 BeadChip platform. Genes related with differentially methylated probes (DMPs) in functionally critical genomic regions, including enhancers, promoters, and DNase hypersensitive sites (DHS) were identified, and submitted to Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
12 Samples
Download data: CSV, IDAT, TXT
Series
Accession:
GSE287809
ID:
200287809
7.

Cross-Tissue Comparison of Epigenetic Aging Clocks in Humans

(Submitter supplied) Epigenetic clocks are a common group of tools used to measure biological aging – the progressive deterioration of cells, tissues and organs. Epigenetic clocks have been trained almost exclusively using blood-based tissues but there is growing interest in estimating epigenetic age using less-invasive oral-based tissues (i.e., buccal or saliva) in both research and commercial settings. However, differentiated cell types across body tissues exhibit unique DNA methylation landscapes and age-related alterations to the DNA methylome. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL33022
163 Samples
Download data: CSV, IDAT
Series
Accession:
GSE280465
ID:
200280465
8.

Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs [RRBS]

(Submitter supplied) Through a multi-omics approach, we discovered that metformin acts by enhancing the methylation potential in Dnmt3aR878H/+ cells and reversing their aberrant DNA CpG methylation and histone H3K27 trimethylation (H3K27me3) profiles.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24247
14 Samples
Download data: TXT
Series
Accession:
GSE255788
ID:
200255788
9.

Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
Platform:
GPL24247
39 Samples
Download data: BW, TXT
Series
Accession:
GSE255101
ID:
200255101
10.

Development of a potent epigenetic editor targeting human PCSK9 with durable reduction of cholesterol in mice and non-human primates [amplicon methylation]

(Submitter supplied) DNA methylation in gene promoter regions is a conserved, innate epigenetic mechanism to control gene expression. Transient application of epigenetic editors designed to induce DNA methylation has been shown to silence genes in cultured cells and in mice. Here we report the development of a potent, efficacious, and specific human PCSK9-targeting epigenetic editor. A single administration of lipid nanoparticles encapsulating mRNA encoding the epigenetic editor which precisely targets the PCSK9 locus was sufficient to drive near-complete silencing in transgenic mice expressing human PCSK9. more...
Organism:
Macaca fascicularis
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL34256
11 Samples
Download data: BEDGRAPH
Series
Accession:
GSE282432
ID:
200282432
11.

Specific modulation of 28S_Um2402 rRNA 2'-O-ribose methylation as a novel epitranscriptomic marker of ZEB1-induced epithelial-mesenchymal transition in different mammary cell contexts.

(Submitter supplied) The epithelial–mesenchymal transition (EMT) is a dynamic transdifferentiation of epithelial cells into mesenchymal cells. EMT programs exhibit great diversity, based primarily on the distinct impact of molecular activities of the EMT transcription factors. Using a panel of cancer cell lines and a series of 71 triple-negative primary breast tumors, we report that the EMT transcription factor ZEB1 modulates site-specific chemical modifications of ribosomal RNA (rRNA). more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24676
35 Samples
Download data: CSV
Series
Accession:
GSE261572
ID:
200261572
12.

Development of a potent epigenetic editor targeting human PCSK9 with durable reduction of cholesterol in mice and non-human primates

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Macaca fascicularis; Mus musculus; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms
96 Samples
Download data: BEDGRAPH, RESULTS
Series
Accession:
GSE282522
ID:
200282522
13.

hMeDIP-seq of mouse cerebellum using nanopore sequencing

(Submitter supplied) 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are modified versions of cytosine in DNA with roles in regulating gene expression. Using whole genomic DNA from mouse cerebellum, we benchmark 5mC and 5hmC detection by Oxford Nanopore Technologies sequencing against other standard techniques. In addition, we assess the ability of duplex base-calling to study strand asymmetric modification. Nanopore detection of 5mC and 5hmC is accurate relative to compared techniques and opens new means of studying these modifications. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24973
3 Samples
Download data: BED, NARROWPEAK
Series
Accession:
GSE288331
ID:
200288331
14.

DNA methylation-based age prediction and sex-specific epigenetic aging in a lizard with female-biased longevity

(Submitter supplied) Sex differences in lifespan are widespread across animal taxa, but their causes remain unresolved. Alterations to the epigenome are hypothesized to contribute to vertebrate aging, and DNA methylation-based aging clocks allow for quantitative estimation of biological aging trajectories. Here, we investigate the influence of age, sex, and their interaction on genome-wide DNA methylation patterns in the brown anole (Anolis sagrei), a lizard with pronounced female-biased survival and longevity. more...
Organism:
Anolis sagrei
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL33576
40 Samples
Download data: TAB
Series
Accession:
GSE285624
ID:
200285624
15.

Characterization of rationally designed CRISPR/Cas9-based DNA methyltransferases with distinct methyltransferase and gene silencing activities in human cell lines and primary human T cells

(Submitter supplied) Nuclease-deactivated Cas (dCas) proteins can be used to recruit epigenetic effectors, and this class of epigenetic editing technologies has revolutionized the ability to synthetically control the mammalian epigenome and transcriptome. DNA methylation is one of the most important and well-characterized epigenetic modifications in mammals, and while many different forms of dCas-based DNA methyltransferases (dCas-DNMTs) have been developed for programmable DNA methylation, these tools are frequently poorly tolerated and/or lowly-expressed in mammalian cell types. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL33022
12 Samples
Download data: CSV, IDAT
Series
Accession:
GSE283742
ID:
200283742
16.

Genomic landscape of DNA methylation following m6A demethylation

(Submitter supplied) ALKBH5 has been recognized as a major RNA m6A demethylase in human cells. Here, we show that genomic DNA methylation is reshaped following the transcriptomic m6a demethylation. ALKBH5-KD human colon cancer cell line HCT116 was constructed. The genomic DNA was extracted to profile the genome-wide methylation.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL21145
6 Samples
Download data: IDAT, XLSX
Series
Accession:
GSE196028
ID:
200196028
17.

Genomic landscape of DNA methylation following APOBEC3A-induced mutation

(Submitter supplied) APOBEC-induced genomic mutation a major driver of cancer evolution. Here, we show that genomic DNA methylation is reshaped following the APOBEC-induced genomic mutation.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL21145
6 Samples
Download data: IDAT, XLSX
Series
Accession:
GSE196027
ID:
200196027
18.

methylGrapher: Genome-Graph-Based Processing of DNA Methylation Data from Whole Genome Bisulfite Sequencing

(Submitter supplied) Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24676
10 Samples
Download data: COV, TXT
Series
Accession:
GSE261315
ID:
200261315
19.

The DNA methylation profiles of 20 healthy controls

(Submitter supplied) Genome wide DNA methylation profiling of 20 healthy individuals. The Illumina Infinium MethylationEPIC array v1 (850K) was used to obtain DNA methylation profiles across approximately 865,000 CpGs in Peripheral blood mononuclear cells.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL21145
20 Samples
Download data: IDAT
Series
Accession:
GSE255776
ID:
200255776
20.

Endocrine islet beta-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients

(Submitter supplied) Endocrine islet beta cells comprise heterogenous cell subsets. Yet the origin, stability, and physiological significance of these subsets remain largely unknown. Using combinatorial cell lineage tracing, scRNA-seq, and DNA methylation analysis, we show here that embryonic islet progenitors with differential gene expression and DNA methylation produce stable beta-cell subtypes of different function and viability in adult mice. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24247
12 Samples
Download data: METH, TXT
Series
Accession:
GSE254955
ID:
200254955
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