Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Kory Johnson

PROVIDER: E-GEOD-51748 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells. [Illumina]

Project description:Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level. 12 samples: 1 human NPC, 5 human ESC (UNDIFF), 6 human iPSC (UNDIFF)

2014-01-01 | E-GEOD-51747 | biostudies-arrayexpress

Dynamics of DNA methylation patterning during in vitro propagation of human spermatogonial stem cells

Project description:Autotransplantation of in vitro proliferated spermatogonial stem cells (SSCs) has been advocated as a way to restore fertility in childhood cancer survivors. In this study we determined the effects of cell culture on DNA methylation patterning in human SSCs, to evaluate the safety of future clinical application of SSC autotransplantation. Bisulfite converted DNA of 34 human spermatogonial stem cell samples, 4 sperm samples and 3 seminoma samples were hybridized to Illumina Infinium 450k Human Methylation Beadchips

2016-02-27 | E-GEOD-72444 | biostudies-arrayexpress

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [III]

Project description:In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response. Bisulphite converted DNA from the 4 samples were hybridized to the Illumina HumanMethylation450 BeadChip (Sample L and SI were examined twice).

2015-06-16 | E-GEOD-67484 | biostudies-arrayexpress

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [II]

Project description:In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response. Bisulphite converted DNA from the 7 samples were hybridized to the Illumina HumanMethylation450 BeadChip.

2015-06-16 | E-GEOD-67477 | biostudies-arrayexpress

Methylation Profiling of Human Kidney Tubules

Project description:We sought to decrease the cell type heterogeneity of kidney tissues to increase the resolution of methylation profiles. To that end, microdissected human kidney tissue from patients are used and hybridized on Illumina HumanMethylation450 BeadChip arrays. We extract genomic DNA from microdissected human kidney tubule samples. And used these genomic DNA for the Illumina 450K beads array.

2013-09-14 | E-GEOD-50874 | biostudies-arrayexpress

Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients

Project description:Recent studies suggest that genetic and environmental factors do not account for all the schizophrenia risk and epigenetics also plays a role in disease susceptibility. DNA methylation is a heritable epigenetic modification that can regulate gene expression. Genome-Wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls. DNA methylation was assessed at over 485 000 CpG sites using the Illumina Infinium Human Methylation450 Bead Chip. After adjusting for age and post-mortem interval (PMI), 4 641 probes corresponding to 2 929 unique genes were found to be differentially methylated. Of those genes, 1 291 were located in a CpG island and 817 were in a promoter region. These include NOS1, AKT1, DTNBP1, DNMT1, PPP3CC and SOX10 which have previously been associated with schizophrenia. More than 100 of these genes overlap with a previous DNA methylation study of peripheral blood from schizophrenia patients in which 27 000 CpG sites were analysed. Unsupervised clustering analysis of the top 3 000 most variable probes revealed two distinct groups with significantly more people with schizophrenia in cluster one compared to controls (p = 1.74x10-4). The first cluster was composed of 88% of patients with schizophrenia and only 12% controls while the second cluster was composed of 27% of patients with schizophrenia and 73% controls. These results strongly suggest that differential DNA methylation is important in schizophrenia etiology and add support for the use of DNA methylation profiles as a future prognostic indicator of schizophrenia Genome-Wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls. DNA methylation was assessed at over 485 000 CpG sites using the Illumina Infinium Human Methylation450 Bead Chip.

2014-09-05 | E-GEOD-61107 | biostudies-arrayexpress

Stress, heritability, tissue type and human methylome variation.

Project description:Genomewide methylation profiles from three tissues (cord blood, placenta, venous blood) derived from 24 mother-child dyads. Data was assayed with the Illumina HumanMethylation 450K Beacdchip and processed with Illumina's GenomeStudio V2011.1 Methylation Module v1.9.0 Bisulfite converted DNA from three tissues derived from 24 dyads, totalling 72 samples, were hybridized to the Illumina HumanMethylation450 BeadChips following the manufacturerÕs specifications.

2014-03-01 | E-GEOD-54399 | biostudies-arrayexpress

Symmetrical dose-dependent DNA methylation profiles in children with deletion or duplication of chromosome 7q11.23

Project description:Genome wide DNA methylation in blood derived DNA from individuals with deletion or duplication of 7q11.23 Bisulfite converted DNA was hybridized onto the Illumina Infinium HumanMethylation450 BeadChip array

2015-07-09 | E-GEOD-66552 | biostudies-arrayexpress

Tissue- and Aging-specific DNA-Methylation Patterns are erased in Mesenchymal Stromal Cells derived from Induced Pluripotent Stem Cells.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-09-24 | E-GEOD-54769 | biostudies-arrayexpress

Profiling Methylomic Alterations in Postmortem Prefrontal Cortex Tissues of Individuals with Alcohol Use Disorders

Project description:Analysis of methylomic alternations related with alcohol use disorders (AUD). The hypothesis is that chronic alcohol consumption might alter genome-wide DNA methylation patterns. The results suggest that differential DNA methylation might be invovled in neuradaptations to alcohol. Genomic DNA was extraced from postmortem prefrontal cortex tissues of 23 AUD cases and 23 matched controls. Both AUD cases and matched controls are assessed with DSM-IV

2013-11-06 | E-GEOD-49393 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data