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GenomicsWidespread targeted chromatin remodeling during the initial phase of somatic cell reprogramming [RRBS]
Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem (iPS) cell state, many mechanistic questions still remain. To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcri...
ORGANISM(S): Mus musculus 
2011-01-03 | E-GEOD-26098 | biostudies-arrayexpress
GenomicsGenome-scale DNA methylation maps of pluripotent and differentiated cells
We report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps covering the vast majority of C...
ORGANISM(S): Mus musculus 
2008-07-06 | E-GEOD-11034 | biostudies-arrayexpress
GenomicsGenome-wide chromatin state maps of ES cells, ES-derived neural progenitor cells and brain tissue
Genome-wide chromatin state maps of murine embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue. The data were generated to examine the correlation between histone and DNA methylation during lineage-commitment. Keywords: High-throughput ChIP-sequencing, Illumina, cell...
ORGANISM(S): Mus musculus 
2008-07-05 | E-GEOD-11172 | biostudies-arrayexpress
GenomicsGenomic distribution and inter-sample variation of non-CG methylation across human cell types
DNA methylation plays an important role in development and disease. The primary sites of DNA methylation in vertebrates are cytosines in the CpG dinucleotide context, which account for roughly three quarters of the total DNA methylation content in human and mouse cells. While the genomic distributio...
ORGANISM(S): Homo sapiens 
2011-08-31 | E-GEOD-27432 | biostudies-arrayexpress
GenomicsA unique regulatory phase of DNA methylation in the early mammalian embryo
DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of global cytosine methylation at fertilization, followed by passive depletion that reaches a minimum at the blastocyst stage. However, this model is based on limit...
ORGANISM(S): Mus musculus 
2012-03-28 | E-GEOD-34864 | biostudies-arrayexpress
ProteomicsHijacking of transcriptional condensates by endogenous retroviruses
Heterochromatin plays essential roles in repressing retrotransposons, e.g. endogenous retroviruses (ERVs) during mammalian development, but the contribution of retrotransposition to lethality observed in embryonic cells deficient for heterochromatin-mediated ERV repression is poorly understood. Here...
ORGANISM(S): Mus musculus (Mouse) 
2022-07-08 | PXD021895 | Pride
Transposable elements Heterochromatin Transcriptional condensates 
ProteomicsDnmt1 has de novo activity targeted to transposable elements
DNA methylation plays a critical role in development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a and 3b. Here we demonstrate that Dnmt1 displays de nov...
ORGANISM(S): Mus musculus (Mouse) 
2021-06-29 | PXD025736 | Pride
Dnmt1 Uhrf1 Retrotransposon Dna methylation 
GenomicsTranscription factor binding dynamics during human ES cell differentiation
Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome wide binding data for 38 transcription factors with extensive epigenome and transcriptional da...
ORGANISM(S): Homo sapiens 
2015-02-19 | E-GEOD-61475 | biostudies-arrayexpress
GenomicsWidespread targeted chromatin remodeling during the initial phase of somatic cell reprogramming [ChIP-Seq]
Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem (iPS) cell state, many mechanistic questions still remain. To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcri...
ORGANISM(S): Mus musculus 
2011-01-03 | E-GEOD-26099 | biostudies-arrayexpress
GenomicsMouse ooplasm confers context-specific reprogramming capacity
Enucleated oocytes have the remarkable ability to reprogram somatic nuclei back to totipotency. Here we investigate genome-scale DNA methylation patterns after nuclear transfer and identify specific targets for DNA demethylation as well as NT specific limitations. We find that the ooplasm can confer...
ORGANISM(S): Mus musculus 
2012-08-10 | E-GEOD-38711 | biostudies-arrayexpress
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