GPL13534[RGSE] - GEO DataSets

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Select item 2002343791.

DNA methylation profile in matched oral cavity squamous cell carcinoma and normal adjacent tissue samples

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a complex and dynamic disease characterized by clinicopathological and molecular heterogeneity. Spatial and temporal heterogeneity of cell subpopulations has been associated with cancer progression and implicated in the prognosis and therapy response. Emerging evidence indicates that aberrant epigenetic profiles in OSCC may foster an immunosuppressive tumor microenvironment by modulating the expression of immune-related long non-coding RNAs (lncRNAs). more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
92 Samples

Download data: IDAT, TXT

Series

Accession:: GSE234379

ID:: 200234379

Select item 2002670152.

MYCN-driven de-differentiation profile identifies a subgroup of aggressive retinoblastoma

(Submitter supplied) Retinoblastoma are childhood eye tumors arising from retinal precursor cells. Two distinct retinoblastoma subtypes with different clinical behavior have been described based on gene expression and methylation profiling. Using consensus clustering of DNA methylation analysis from retinoblastomas, we identified a MYCN-driven cluster of subtype 2 retinoblastomas characterized by DNA hypomethylation and high expression of genes involved in protein synthesis. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platforms:: GPL21145 GPL13534
70 Samples

Download data: IDAT, TXT

Series

Accession:: GSE267015

ID:: 200267015

Select item 2002248503.

H1FOO-DD promotes efficiency and uniformity in reprogramming to naive pluripotency

(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

6 related Platforms
168 Samples

Download data: BED, IDAT, MTX, TSV, TXT

Series

Accession:: GSE224850

ID:: 200224850

Select item 2002246974.

DNA methylation analysis of human primed and naive pluripotent stem cells

(Submitter supplied) Human pluripotent stem cells have two major pluripotent states, primed and naive, and the heterogeneity among cell lines in each pluripotent state remains a major unresolved problem. We showed that the overexpression of H1FOO-DD, which has a short expression period by fusing the destabilized domain to the maternal-specific linker histone H1FOO, together with OCT4, SOX2, KLF4 and LMYC in human somatic cells improves the quality of reprogramming to primed and naive pluripotency.

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platforms:: GPL13534 GPL21145
48 Samples

Download data: IDAT, TXT

Series

Accession:: GSE224697

ID:: 200224697

Select item 2002224785.

Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [methylation 1]

(Submitter supplied) Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platforms:: GPL13534 GPL23976
40 Samples

Download data: IDAT

Series

Accession:: GSE222478

ID:: 200222478

Analyze with GEO2R

Select item 2002437966.

Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level

(Submitter supplied) Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies – mainly studying nucleic acids – has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. more...

Organism:: Homo sapiens

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

Platforms:: GPL23976 GPL30173 GPL13534
90 Samples

Download data: IDAT

Series

Accession:: GSE243796

ID:: 200243796

Analyze with GEO2R

Select item 2002471987.

Epigenetic age oscillates during the day

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

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platforms:: GPL21145 GPL13534
96 Samples

Download data: IDAT

Series

Accession:: GSE247198

ID:: 200247198

PubMed Similar studies

Select item 2002471978.

Epigenetic age oscillates during the day (WBC-Neu 52 yr old)

(Submitter supplied) Since their introduction, epigenetic clocks have been extensively used in aging and human disease research. In this study, we reveal an intriguing pattern: epigenetic age predictions display a 24-hour periodicity. These paradoxical age oscillations can be attributed to variations in blood cell type composition and epigenomes, both of which demonstrate circadian rhythmicity. This discovery emphasizes the significance of factoring-in the time of day to obtain accurate estimates of epigenetic age.

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
48 Samples

Download data: IDAT, TXT

Series

Accession:: GSE247197

ID:: 200247197

PubMed Similar studies

Select item 2002268189.

DNA methylation profiles in gastric mucosa samples with low, intermediate and high cancer risk

(Submitter supplied) DNA methylation profiles were compared between gastric mucosae samples without Helicobacter pylori (HP) infection (low risk : G1), those with HP eradication without gastric cancer (intermediate risk : G2), and those with HP eradication with gastric cancer (high risk : G3).

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
8 Samples

Download data: TXT

Series

Accession:: GSE226818

ID:: 200226818

Analyze with GEO2R

Select item 20026252210.

Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer [m450K]

(Submitter supplied) Prostate cancer incidence and related mortality are disproportionately higher in African American (AA) men than European American (EA) men, but the molecular mechanisms contributing to racial disparities are not fully elucidated. To identify molecular factors that can contribute to disease biology in prostate cancer from AA and EA men, we utilized a multi-omics approach to measure and integrate DNA methylation with gene expression changes. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
68 Samples

Download data: IDAT, TSV

Series

Accession:: GSE262522

ID:: 200262522

PubMed Full text in PMC Similar studies

Select item 20024963711.

Phenotypical states modulate sensitivity and transcriptional reprogramming in patient-derived glioblastoma cells in response to temozolomide and radiation therapy.

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

Organism:: Homo sapiens

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

Platforms:: GPL16791 GPL13534
84 Samples

Download data: IDAT

Series

Accession:: GSE249637

ID:: 200249637

Analyze with GEO2R

Select item 20024963612.

Phenotypical states modulate sensitivity and transcriptional reprogramming in patient-derived glioblastoma cells in response to temozolomide and radiation therapy. [array]

(Submitter supplied) Genome wide DNA methylation profiling of patient-derived glioblastoma cells cultured as neurospheres or FBS differentited cells. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in glioblastoma CSCs and serum differentiated cells treated with 4 Gy ionizing radiation or IC30 concentration of temozolomide as well as vehicle control samples. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
36 Samples

Download data: IDAT

Series

Accession:: GSE249636

ID:: 200249636

Analyze with GEO2R

Select item 20013131813.

Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers

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

Organism:: Homo sapiens

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

4 related Platforms
77 Samples

Download data: BW, IDAT

Series

Accession:: GSE131318

ID:: 200131318

Analyze with GEO2R

Select item 20013131214.

Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [450k array]

(Submitter supplied) In the present study, we applied two whole-genome sequencing techniques (WGBS/oxBS and hMe-Seal) to detect 5hmC (and 5mC) changes during the differentiation of the human SGBS preadipocyte cell line to mature adipocytes. As technical and biological validation we performed BS and oxBS followed by 450k array analysis. RNA-seq data was performed in parallel to study transcriptional changes associated with differential hydroxymethylation. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
22 Samples

Download data: IDAT

Series

Accession:: GSE131312

ID:: 200131312

Analyze with GEO2R

Select item 20024881115.

Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology.

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

Organism:: Homo sapiens

Type:: Methylation profiling by array; Other

Platforms:: GPL13534 GPL21145 GPL24676
128 Samples

Download data: DCC, IDAT

Series

Accession:: GSE248811

ID:: 200248811

PubMed Full text in PMC Similar studies

Select item 20024861816.

Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology

(Submitter supplied) Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences between these morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platforms:: GPL13534 GPL21145
79 Samples

Download data: CSV, IDAT, RDS

Series

Accession:: GSE248618

ID:: 200248618

PubMed Full text in PMC Similar studies

Select item 20024324017.

Molecular characteristics and improved survival prediction in a cohort of 2023 ependymomas

(Submitter supplied) The diagnosis of ependymoma has moved from a purely histopathological review with limited prognostic value to an integrated diagnosis, relying heavily on molecular information. However, as the integrated approach is still novel and some molecular ependymoma subtypes are quite rare, few studies have correlated integrated pathology and clinical outcome, often focusing on small series of single molecular types. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array; Third-party reanalysis

Platforms:: GPL21145 GPL13534
287 Samples

Download data: IDAT, TXT, XLS

Series

Accession:: GSE243240

ID:: 200243240

PubMed Full text in PMC Similar studies

Select item 20024299418.

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array; Other

Platforms:: GPL13534 GPL21145 GPL24676
294 Samples

Download data: IDAT, TSV, XLSX

Series

Accession:: GSE242994

ID:: 200242994

PubMed Full text in PMC Similar studies

Select item 20024299119.

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations [Methylation]

(Submitter supplied) Background: Ependymomas encompass multiple, clinically relevant tumor types based on localization and molecular profiles. Although tumors of the methylation class “spinal ependymoma” (SP-EPN) represent the most common intramedullary neoplasms in children and adults, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. more...