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TranscriptomicsApplication of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution.
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 scie...
ORGANISM(S): Homo sapiens 
2014-12-12 | E-GEOD-60225 | biostudies-arrayexpress
TranscriptomicsRecurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives
This SuperSeries is composed of the following subset Series: GSE30652: Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina HT12v3 Gene Expression] GSE30653: Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and ...
ORGANISM(S): Homo sapiens 
2012-05-13 | E-GEOD-30654 | biostudies-arrayexpress
TranscriptomicsEpigenetic therapy for Friedreich ataxia.
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, H...
ORGANISM(S): Homo sapiens 
2015-01-29 | E-GEOD-65399 | biostudies-arrayexpress
TranscriptomicsRecurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 450K DNA Methylation]
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 s...
ORGANISM(S): Homo sapiens 
2012-05-13 | E-GEOD-31848 | biostudies-arrayexpress
TranscriptomicsRecurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 27K DNA Methylation]
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 s...
ORGANISM(S): Homo sapiens 
2012-05-13 | E-GEOD-30653 | biostudies-arrayexpress
TranscriptomicsDynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation (mRNA)
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 char...
ORGANISM(S): Homo sapiens 
2012-11-07 | E-GEOD-42094 | biostudies-arrayexpress
TranscriptomicsDynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation (miRNA)
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 char...
ORGANISM(S): Homo sapiens 
2012-11-07 | E-GEOD-42093 | biostudies-arrayexpress
TranscriptomicsBMP4-directed trophoblast differentiation of human embryonic stem cells is mediated through a ΔNp63+ cytotrophoblast stem cell state
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. We have compared gene expression profiling of FCM-BMP4-treated hESC to a panel of fetal tissues and first trimester tissues. ...
ORGANISM(S): Homo sapiens 
2013-11-05 | E-GEOD-49354 | biostudies-arrayexpress
TranscriptomicsDistinct classes of genes behave as either drivers or dependents of replication timing switches (Replication-Timing).
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 trans...
ORGANISM(S): Homo sapiens 
2015-05-28 | E-GEOD-63428 | biostudies-arrayexpress
TranscriptomicsInduced pluripotent stem cell-derived models of sporadic and familial Alzheimer’s disease
Our understanding of Alzheimer’s disease (AD) pathogenesis is currently limited by difficulties in obtaining live neurons from patients and the inability to model the sporadic form of AD. It may be possible to overcome these challenges by reprogramming primary cells from patients into induced plurip...
ORGANISM(S): Homo sapiens 
2012-01-06 | E-GEOD-34879 | biostudies-arrayexpress
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