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GenomicsIdentification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells
In this work, we characterized the epigenomic integrity of 17 hiPSC lines derived from six different cell types with varied reprogramming efficiencies. We demonstrate that epigenetic aberrations are a general feature of the hiPSC state and are independent of the somatic cell source. Additionally, we...
ORGANISM(S): Homo sapiens 
2012-08-28 | E-GEOD-40372 | biostudies-arrayexpress
GenomicsTranscriptome profiling of wild type and Tet1-null primordial germ cells (PGC) by Bisulfite-seq
Purpose: To investigate the effect of Tet1 depletion on global DNA methylation, we performed whole-genome bisulfite sequencing (WGBS). Methods: Starting with as little as 1400-5251 manually micro-dissected PGCs, we used an ultra-low input method, Tn5mC-seq. Results: We generated 945 million reads fo...
ORGANISM(S): Mus musculus 
2012-11-20 | E-GEOD-41912 | biostudies-arrayexpress
TranscriptomicsTranscriptome profiling of wild type primordial germ cells (PGC) by RNAseq
Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing. Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), w...
ORGANISM(S): Mus musculus 
2012-10-31 | E-GEOD-41908 | biostudies-arrayexpress
GenomicsModeling Fanconi Anemia pathogenesis and therapeutics using integration-free patient iPSCs
To elucidate the transcriptional and epigenetic alterations underlying the neurogenic defects of FA-NSCs, we conducted gene expression microarray analysis and global DNA methylation profiling. The gene expression pattern of gene-corrected NSCs (C-FA-NSCs) resembled that of control-NSCs but clustered...
ORGANISM(S): Homo sapiens 
2014-05-15 | E-GEOD-57685 | biostudies-arrayexpress
GenomicsGenome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [MeDIP-Seq]
Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carboxylcytosine (5caC) through iterative oxidation reactions. While 5mC and 5hmC are relatively abundant, 5fC and 5caC are at very low levels...
ORGANISM(S): Mus musculus 
2013-04-18 | E-GEOD-46111 | biostudies-arrayexpress
UnknownPressor response to angiotensin II is enhanced in aged mice and associated with inflammation, vasoconstriction and oxidative stress.
Not available
S-EPMC5509458 | biostudies-literature
TranscriptomicsRecapitulation of human premature aging by using iPSCs from Hutchinson-Gilford progeria syndrome
Hutchinson-Gilford progeria syndrome (HGPS) is a rare and fatal human premature aging disease1-5, characterized by premature atherosclerosis and degeneration of vascular smooth muscle cells (SMCs)6-8. HGPS is caused by a single-point mutation in the LMNA gene, resulting in the generation of progerin...
ORGANISM(S): Homo sapiens 
2011-03-14 | E-GEOD-24487 | biostudies-arrayexpress
UnknownHuman amnion epithelial cell therapy reduces hypertension-induced vascular stiffening and cognitive impairment.
Not available
S-EPMC10800338 | biostudies-literature
TranscriptomicsGenome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [Expression]
Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carboxylcytosine (5caC) through iterative oxidation reactions. While 5mC and 5hmC are relatively abundant, 5fC and 5caC are at very low levels...
ORGANISM(S): Mus musculus 
2013-04-18 | E-GEOD-46112 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics
Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carboxylcytosine (5caC) through iterative oxidation reactions. While 5mC and 5hmC are relatively abundant, 5fC and 5caC are at very low levels...
ORGANISM(S): Mus musculus 
2013-04-18 | E-GEOD-42250 | biostudies-arrayexpress
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