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1.

Tumor hypoxia causes DNA hypermethylation by reducing TET activity (BeadChip)

(Submitter supplied) Genome wide DNA methylation profiling of normoxic and hypoxic non-small-cell lung cancer samples for 5mC and 5hmC. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation and hydroxymethylation profiles across 485,512 CpGs from DNA extracted from fresh-frozen tumor samples. Samples included 12 hypoxic and 12 normoxic tumor samples, with hypoxia determined according to the hypoxia metagene score (Buffa et al, Br J Cancer 2010). more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL16304
48 Samples
Download data: IDAT, TXT
Series
Accession:
GSE71398
ID:
200071398
2.

Human Stem Cells from Single Blastomeres Reveal Pathways of Embryonic or Trophoblast Fate Specification.

(Submitter supplied) Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple (UCSFB1-10). Versus numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns, in part, indicative of trophoblast competence. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL6947 GPL13534 GPL10558
383 Samples
Download data: TXT
Series
Accession:
GSE72923
ID:
200072923
3.

DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array; Expression profiling by array
Platforms:
GPL13667 GPL13534
64 Samples
Download data: CEL
Series
Accession:
GSE54721
ID:
200054721
4.

DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [gene expression]

(Submitter supplied) DNA methylation changes in neuroblastoma, a clinically-heterogeneous pediatric tumor, have been described essentially in promoter regions. We analyzed the DNA methylome of neuroblastoma using high-density microarrays and observed differential methylation not only in promoters but also in intragenic and intergenic regions at both CpG and non-CpG sites. These epigenetic changes showed a non-random distribution relative functional chromatin domains, and targeted development and cancer-related genes, relevant for neuroblastoma pathogenesis. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL13667
23 Samples
Download data: CEL
Series
Accession:
GSE54720
ID:
200054720
5.

DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [methylation]

(Submitter supplied) DNA methylation changes in neuroblastoma, a clinically-heterogeneous pediatric tumor, have been described essentially in promoter regions. We analyzed the DNA methylome of neuroblastoma using high-density microarrays and observed differential methylation not only in promoters but also in intragenic and intergenic regions at both CpG and non-CpG sites. These epigenetic changes showed a non-random distribution relative functional chromatin domains, and targeted development and cancer-related genes, relevant for neuroblastoma pathogenesis. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
41 Samples
Download data: TXT
Series
Accession:
GSE54719
ID:
200054719
6.

Distinct classes of genes behave as either drivers or dependents of replication timing switches.

(Submitter supplied) Duplication of the genome in mammalian cells occurs in a defined temporal order referred as its replication-timing program (RT). RT is regulated in units of 400-800 Kb referred as replication domains (RDs) and changes dynamically during development. Changes in RT are generally coordinated with transcriptional competence and changes in sub-nuclear position. We generated genome-wide RT profiles for 29 distinct human cell types including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm and neural crest (NC) development. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
64 Samples
Download data: TXT
Series
Accession:
GSE63592
ID:
200063592
7.

Distinct classes of genes behave as either drivers or dependents of replication timing switches (Replication-Timing).

(Submitter supplied) Duplication of the genome in mammalian cells occurs in a defined temporal order referred as its replication-timing program (RT). RT is regulated in units of 400-800 Kb referred as replication domains (RDs) and changes dynamically during development. Changes in RT are generally coordinated with transcriptional competence and changes in sub-nuclear position. We generated genome-wide RT profiles for 29 distinct human cell types including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm and neural crest (NC) development. more...
Organism:
Homo sapiens
Type:
Other
4 related Platforms
60 Samples
Download data: PAIR
Series
Accession:
GSE63428
ID:
200063428
8.

Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions I

(Submitter supplied) The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them good sources of cells for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array; SNP genotyping by SNP array; Genome variation profiling by SNP array
Platforms:
GPL6884 GPL8882 GPL13534
183 Samples
Download data: TXT
Series
Accession:
GSE34982
ID:
200034982
9.

Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions II

(Submitter supplied) The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them good sources of cells for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL14157
9 Samples
Download data: TXT
Series
Accession:
GSE56834
ID:
200056834
10.

Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array; SNP genotyping by SNP array; Genome variation profiling by SNP array
4 related Platforms
192 Samples
Download data
Series
Accession:
GSE56851
ID:
200056851
11.

Epigenetic therapy for Friedreich ataxia.

(Submitter supplied) We set out to investigate whether a histone deacetylase inhibitor (HDACi) would be effective in an in vitro model for the neurodegenerative disease Friedreich ataxia (FRDA) and to evaluate safety and surrogate markers of efficacy in a phase I clinical trial in patients. In the neuronal cell model, HDACi 109/RG2833 increases FXN mRNA levels and frataxin protein, with concomitant changes in the epigenetic state of the gene. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
75 Samples
Download data: TXT
Series
Accession:
GSE65399
ID:
200065399
12.

Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution.

(Submitter supplied) 5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use cost-prohibitive DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community. Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
18 Samples
Download data: TXT
Series
Accession:
GSE60225
ID:
200060225
13.

BMP4-directed trophoblast differentiation of human embryonic stem cells is mediated through a ΔNp63+ cytotrophoblast stem cell state

(Submitter supplied) We show that FCM-BMP4-treated hESC differentiate into bona fide CTB by direct comparison to primary human placental tissues and isolated CTB through gene expresson profiling.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
126 Samples
Download data: TXT
Series
Accession:
GSE49354
ID:
200049354
14.

Dynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by array; Expression profiling by array
Platforms:
GPL8179 GPL10558
46 Samples
Download data
Series
Accession:
GSE42095
ID:
200042095
15.

Dynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation (mRNA)

(Submitter supplied) The remarkable differentiation capacity of pluripotent stem cells into any adult cell types have enabled researchers to model human embryonic development and disease process in dishes, as well as deriving specialized cells for replacing damaged tissues. Type 1 diabetes is a degenerative disease characterized by autoimmune destruction of the insulin-producing beta islet cells in the pancreas. Recent advances have led to the establishment of different methods to direct differentiation of human or mouse pluripotent stem cells toward beta cell lineages. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
23 Samples
Download data: TXT
Series
Accession:
GSE42094
ID:
200042094
16.

Dynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation (miRNA)

(Submitter supplied) The remarkable differentiation capacity of pluripotent stem cells into any adult cell types have enabled researchers to model human embryonic development and disease process in dishes, as well as deriving specialized cells for replacing damaged tissues. Type 1 diabetes is a degenerative disease characterized by autoimmune destruction of the insulin-producing beta islet cells in the pancreas. Recent advances have led to the establishment of different methods to direct differentiation of human or mouse pluripotent stem cells toward beta cell lineages. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL8179
23 Samples
Download data: TXT
Series
Accession:
GSE42093
ID:
200042093
17.

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by array
Platforms:
GPL8490 GPL6947 GPL13534
675 Samples
Download data
Series
Accession:
GSE30654
ID:
200030654
18.

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 27K DNA Methylation]

(Submitter supplied) Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL8490
283 Samples
Download data: TXT
Series
Accession:
GSE30653
ID:
200030653
19.

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina HT12v3 Gene Expression]

(Submitter supplied) Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6947
239 Samples
Download data: TXT
Series
Accession:
GSE30652
ID:
200030652
20.

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 450K DNA Methylation]

(Submitter supplied) Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
153 Samples
Download data: TXT
Series
Accession:
GSE31848
ID:
200031848
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db=gds|term=Kristopher%20Nazor|query=1|qty=2|blobid=NCID_1_189870943_130.14.18.125_9001_1537869684_10480308_0MetA0_S_MegaStore_F_1|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
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