GEO DataSets

(Submitter supplied) Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. DNA and chromatin modifications form barriers to the genomic binding of TFs, however, the details of how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci remain unknown. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL24247

27 Samples

Download data: BW

(Submitter supplied) Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. DNA and chromatin modifications form barriers to the genomic binding of TFs, however, the details of how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci remain unknown. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BW

(Submitter supplied) Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. DNA and chromatin modifications form barriers to the genomic binding of TFs, however, the details of how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci remain unknown. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BW

(Submitter supplied) Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. DNA and chromatin modifications form barriers to the genomic binding of TFs, however, the details of how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci remain unknown. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: BW

(Submitter supplied) Wilms tumor (WT), also known as nephroblastoma, is the most commonly observed renal tumor within the genitourinary tract of children and constitutes 5% of all childhood malignancies. In this study, we used microarray technology to explore methylation patterns in both WT and adjacent healthy tissues from excised kidneys prior to any chemotherapy treatment in stage I and II WTs. We report several differentially methylated regions that show potential as prognostic biomarkers for disease relapse, and overall patient survival. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Transcription factors guide tissue development by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of transcription factors. However, how transcription factors navigate chromatin features to selectively bind a small subset of all the possible genomic target loci remains poorly understood. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL24247 GPL24676

43 Samples

Download data: BW

(Submitter supplied) DNA methylation profiling of the entire genome of articular cartilage extracted from human foetal samples across a range of gestational periods. Profiling of 72 samples was performed with Illumina HumanMethylation850 EPIC v1.0 microarrays, measuring methylation at approximately 850K sites.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

72 Samples

Download data: IDAT, TSV

(Submitter supplied) To define the epigenetic signature of human DCregs generated in vitamin 14 D3 (vitD3) and IL-10 compared to immune stimulatory DCs (sDCs), we measured levels of DNA methylation by whole genome bisulfite sequencing (WGBS). Distinct DNA methylation patterns were acquired by DCregs compared to sDCs. These patterns were located mainly in transcriptional regulatory regions. Genes associated with these programs were enriched in STAT3-signaling and valine catabolism in DCregs; conversely, pro-inflammatory pathways e.g., pattern recognition receptor signaling, were enriched in sDCs. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: COV, XLSX

(Submitter supplied) Temozolomide (TMZ) is an important first-line treatment for glioblastoma (GBM), but there are limitations to TMZ response in terms of durability and dependence on the promoter methylation status of the DNA repair gene O6-methylguanine DNA methyltransferase (MGMT). MGMT-promoter-hypermethylated (MGMT-M) GBMs are more sensitive to TMZ than MGMT-promoter-hypomethylated (MGMT-UM) GBMs. Moreover, TMZ resistance is inevitable even in TMZ-sensitive MGMT-M GBMs. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT, TXT

(Submitter supplied) The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. more...

Organism:

Ptychidio jordani

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL35114

1 Sample

Download data: TXT

(Submitter supplied) The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. more...

Organism:

Ptychidio jordani

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35113

7 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of rhabdomuyosarcoma tumors derived from genetically engineered mouse models. The Illumina MouseMethylation285 BeadChip was used to obtain DNA methylation profiles across approximately 285,000 methylation sites in 31 freshly-frozen rhabdomyosarcoma tumors.

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL31950

31 Samples

Download data: CSV, IDAT

(Submitter supplied) Type 1 diabetes (T1D) is a chronic autoimmune disease resulting from the destruction of insulin-producing beta cells. This persistence is due to the continual replenishment of short-live effector CD8+ T cells (autoimmune mediators, Tmed) in the pancreatic lymph nodes (pLNs) by a long-lived reservoir of stem-like memory CD8+ T cells (autoimmune progenitors, Tprog). We are investigating an epigenetic regulator UTX playing the role in Tprog to Tmed conversion. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34290

6 Samples

Download data: TXT

(Submitter supplied) Malignant peripheral nerve sheath tumor (MPNST) development is characterized by an altered DNA methylation landscape, which presents a promising area for developing MPNST‐specific biomarkers for screening patients with NF1. Genome‐wide DNA methylation profiling of a cohort of 13 patients with MPNST (29 samples of tumor and adjacent neurofibroma tissues) and of NF1‐MPNST cell lines was performed to identify and validate candidate MPNST‐specific CpG sites (CpGs). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

43 Samples

Download data: IDAT, TXT

(Submitter supplied) Differentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic dysregulation by environmental exposures throughout life results in the formation of common chronic diseases. Unfortunately, existing Infinium methylation arrays lack the ability to profile these regions adequately. Whole genome bisulfite sequencing (WGBS) is the unique method able to profile these regions, but it is very expensive and it requires not only a high coverage but it is also computationally intensive to assess those To address this deficiency, we developed a custom methylation array containing 22,819 probes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL34511

16 Samples

Download data: IDAT

(Submitter supplied) Differentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic dysregulation by environmental exposures throughout life results in the formation of common chronic diseases. Unfortunately, existing Infinium methylation arrays lack the ability to profile these regions adequately. Whole genome bisulfite sequencing (WGBS) is the unique method able to profile these regions, but it is very expensive and it requires not only a high coverage but it is also computationally intensive to assess those To address this deficiency, we developed a custom methylation array containing 22,819 probes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL34511

16 Samples

Download data: IDAT

(Submitter supplied) Differentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic dysregulation by environmental exposures throughout life results in the formation of common chronic diseases. Unfortunately, existing Infinium methylation arrays lack the ability to profile these regions adequately. Whole genome bisulfite sequencing (WGBS) is the unique method able to profile these regions, but it is very expensive and it requires not only a high coverage but it is also computationally intensive to assess those To address this deficiency, we developed a custom methylation array containing 22,819 probes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL34511

34 Samples

Download data: IDAT

(Submitter supplied) Differentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic dysregulation by environmental exposures throughout life results in the formation of common chronic diseases. Unfortunately, existing Infinium methylation arrays lack the ability to profile these regions adequately. Whole genome bisulfite sequencing (WGBS) is the unique method able to profile these regions, but it is very expensive and it requires not only a high coverage but it is also computationally intensive to assess those To address this deficiency, we developed a custom methylation array containing 22,819 probes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL34510

3 Samples

Download data: IDAT

(Submitter supplied) The m6A RNA demethylase Fat mass and obesity-associated protein (FTO) is aberrantly upregulated in numerous cancers and promotes tumor development and therapeutic resistance. Here, using public datasets and screening, we show that FTO is ubiquitinated at lysine 162 by its E3 ligase DTX2, followed by recognition by UFD1, leading to degradation in the proteasomes. Furthermore, we identified vitamin E succinate (VES) as a natural first-in-class degrader for FTO by binding to FTO and DTX2, thus enhancing FTO-DTX2 interaction, leading to increased FTO ubiquitination and degradation and enhanced anti-tumor immunity and response to immunotherapy. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TXT

(Submitter supplied) Nanoparticles (NPs) can serve as efficient carriers for delivery of genetic materials in plants. They can regulate normal growth and development, and responses to stresses in plants. However, epigenetic mechanisms underlying NPs or carbon dots (CDs) affecting plant growth and development are still largely unknown. Here we showed that CDs reprogrammed gene transcription associated with some biological processes such as stress responses and photosynthesis. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL27860

8 Samples

Download data: BW, CGMAP, XLS