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GenomicsDetailed analysis of the genetic and epigenetic signature of iPS cell-derived mesodiencephalic dopaminergic neurons
Induced pluripotent stem cells (iPSCs) harbor great promise for in vitro generation of disease-relevant cell types, such as mesodiencephalic dopaminergic (mdDA) neurons involved in Parkinson’s disease. Although iPSC-derived midbrain DA neurons have been generated, detailed genetic and epigenetic cha...
ORGANISM(S): Mus musculus 
2014-03-01 | E-GEOD-55475 | biostudies-arrayexpress
GenomicsSingle-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity
We report a single-cell whole-genome bisulfite sequencing method (scBS-Seq) capable of accurately measuring DNA methylation at up to 36% of CpGs. We observed that ESCs grown in serum/LIF or 2i/LIF both display epigenetic heterogeneity, with M-bM-^@M-^\2i-likeM-bM-^@M-^] cells present in serum cultur...
ORGANISM(S): Mus musculus 
2014-07-18 | E-GEOD-56879 | biostudies-arrayexpress
GenomicsParallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [Bisulfite-Seq]
We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. ...
ORGANISM(S): Mus musculus 
2015-12-24 | E-GEOD-68642 | biostudies-arrayexpress
TranscriptomicsKC002-EH005: Genetic and epigenetic features of induced pluripotent stem cell-derived dopaminergic neurons
Induced pluripotent stem cells (iPSCs) hold great promise for in vitro disease modeling and cell replacement therapy for Parkinson’s disease (PD). Both applications crucially require an in-depth profiling of the disease-relevant, iPSC-derived cell type. Midbrain dopaminergic (mDA) neurons derived fr...
ORGANISM(S): Mus musculus 
2014-05-13 | E-GEOD-47178 | biostudies-arrayexpress
TranscriptomicsDeep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape.
We have performed deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This revealed thousands of novel non-annotated genes as well as alternative promoters for ~10% of reference genes expressed in oocytes, a large fraction of which coincide with transposable eleme...
ORGANISM(S): Mus musculus 
2015-09-02 | E-GEOD-70116 | biostudies-arrayexpress
TranscriptomicsParallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [RNA-seq]
We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. ...
ORGANISM(S): Mus musculus 
2015-12-24 | E-GEOD-74534 | biostudies-arrayexpress
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