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TranscriptomicsRNA-Seq of cKIT+ sorted cells from 16-16.5 week old fetal testes and ovaries and RNA-Seq of TRA-1-60+ H1 hESCs
Generation of research quality, clinically relevant cell types in vitro from human pluripotent stem cells (hPSCs) requires detailed understanding of the equivalent cell types in humans. Here we analyzed 130 human fetal samples at 6-20 weeks of development and identified the stages in which human cKI...
ORGANISM(S): Homo sapiens 
2012-08-03 | E-GEOD-39821 | biostudies-arrayexpress
GenomicsWhole Genome Bisulfite Sequencing (WGBS) of cKIT+ sorted cells from 57-137 day old fetal testes and ovaries.
We performed WGBS analyses on 6 human fetal samples at 53-137 days of development, 4 female and 2 male. We show that methylation reprogramming in the human germline is global yet incomplete with exons, 3’UTRs and human-specific transposons remaining methylated. Whole Genome Bisulfite-Seq of cKIT+ ce...
ORGANISM(S): Homo sapiens 
2015-05-28 | E-GEOD-63393 | biostudies-arrayexpress
GenomicsBisulfite-Seq profiling of undifferentiated ESCs, and in vitro derived primordial germ cells (iPGCs)
We report that in vitro derived PGCs undergo genome-wide DNA demethylation and that this demethylation does not require Tet1/Tet2 Examination of methylation in ESCs, iPGCs, and Tet2-/- iPGCs depleted of Tet1 by shRNA lentiviruses
ORGANISM(S): Mus musculus 
2013-02-14 | E-GEOD-44092 | biostudies-arrayexpress
TranscriptomicsExpression data from SSEA1+ c-kit+ differentiated murine embryonic stem cells
SSEA1+ c-kit+cells sorted from mouse embryonic stem cells differentiated for 4 days in 10uM Retinoic acid do not form teratomas when transplated into SCID mice while Pten-/- cells do. We used microarrays to identify genes and pathways besides Pten that could explain this difference in tumorigenicity...
ORGANISM(S): Mus musculus 
2010-11-19 | E-GEOD-25465 | biostudies-arrayexpress
TranscriptomicsExpression data from SSEA1+ differentiated murine embryonic stem cells
SSEA1+ cells sorted from mouse embryonic stem cells differentiated for 4 days in 10uM Retinoic acid do not form teratomas when transplated into SCID mice while Pten-/- cells do. We used microarrays to identify genes and pathways besides Pten that could explain this difference in tumorigenicity. Key...
ORGANISM(S): Mus musculus 
2010-09-11 | E-GEOD-24078 | biostudies-arrayexpress
GenomicsRelationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq
Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By com...
ORGANISM(S): Homo sapiens 
2010-05-29 | E-GEOD-21821 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human late passage hiPSCs (pluripotent stem cells)
Detailed analysis comparing induced pluripotent stem cells revealed functional gene expression differences to hESCs that are changed with long term passaging. We used microarrays to detail the changes that are made throughout passaging to hiPSC lines. Experiment Overall Design: hiPSC lines were harv...
ORGANISM(S): Homo sapiens 
2009-07-19 | E-GEOD-16654 | biostudies-arrayexpress
GenomicsIn vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse (ChIP-Seq yeast)
Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerev...
ORGANISM(S): Saccharomyces cerevisiae 
2015-04-02 | E-GEOD-66909 | biostudies-arrayexpress
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