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GenomicsSequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequencing (ChIP- BS-seq) as an approach to quantitatively ...
ORGANISM(S): Homo sapiens 
2012-03-27 | E-GEOD-28254 | biostudies-arrayexpress
GenomicsChIP-Seq sequencing of novel interactors of H3K4me3, H3K36me3 and H3K9me3
This study describes the epigenetic profiling of the novel interactors of H3K4me3, H3K36me3 or H3K9me3. The interactors were ChIP-Seq profiled by their GFP tag in stably transfected HeLa (Kyoto) cells. The interactors include GATAD1, Sgf29, BAP18, TRRAP, PHF8, N-PAC and LRWD1 (including replicates),...
ORGANISM(S): Homo sapiens 
2010-09-17 | E-GEOD-20303 | biostudies-arrayexpress
TranscriptomicsP. falciparum Heterochromatin Protein 1 Marks Genomic Loci Linked to Phenotypic Variation of Exported Virulence Factors
Epigenetic processes are the main conductors of phenotypic variation in eukaryotes. The malaria parasite Plasmodium falciparum employs antigenic variation of the major surface antigen PfEMP1, encoded by 60 var genes, to evade acquired immune responses. PfEMP1 also mediates sequestration of infected ...
ORGANISM(S): Plasmodium falciparum 
2010-05-06 | E-GEOD-17029 | biostudies-arrayexpress
ProteomicsA mass spectrometry survey of chromatin-associated proteins in pluripotency and early lineage commitment
Pluripotent Embryonic Stem Cells (ESCs) can be captured in vitro in different states, ranging from unrestricted ‘naïve’ to more developmentally constrained ‘primed’ pluripotency. Complexes involved in epigenetic regulation and key transcription factors have been shown to be involved in specifying th...
ORGANISM(S): Mus musculus (Mouse) 
2019-07-04 | PXD011782 | Pride
Differentiation Naïve pluripotency Lc-ms Primed pluripotency Mouse Chromatin 
ProteomicsQuantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in ground state pluripotency
The ground state of pluripotency is defined as a minimal unrestricted state as present in the Inner Cell Mass (ICM). Mouse embryonic stem cells (ESCs) grown in a defined serum-free medium with two kinase inhibitors (‘2i’) reflect this state, whereas ESCs grown in the presence of serum (‘serum’) shar...
ORGANISM(S): Mus musculus (Mouse) 
2018-11-07 | PXD009217 | Pride
Embryonic stem cells Naïve pluripotency Metabolism Silac 
ProteomicsMethylome profiling of SetDB1 deficient ESCs reveals coordinated epigenetic cross-talk during pluripotency
SetDB1 is best known as a chromatin modifier catalyzing H3K9me3. However, recent studies show that SetDB1 can mediate H3K27me3-deposition by PRC2, CTCF-binding, recruit DNA methyltransferases, and potentially regulate additional chromatin processes. To gain further insights, we profiled the protein ...
ORGANISM(S): Homo sapiens (Human) 
2026-08-20 | PXD074363 | Pride
Hela Pulldown Epigenetics Co-immunoprecipitation Nuclear extract Gfp Chromatin Setdb1 
GenomicsHigh resolution analysis of epigenetic changes associated with X inactivation, ChIP-Seq
This study describes the epigenetic profiling of the X chromosome during X inactivation. It includes H3K4me3 and H3K27me3 ChIP-Seq profiles of male (E14) and female (LF2 and XT67E1) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB). It also includes ChIP-chip ...
ORGANISM(S): Mus musculus 
2009-06-06 | E-GEOD-15814 | biostudies-arrayexpress
ProteomicsMethylome profiling of SetDB1 deficient ESCs reveals coordinated epigenetic cross-talk during pluripotency
In pluripotent mouse embryonic stem cells (ESCs), SetDB1, which targets up to twenty thousand genomic loci, plays an essential role in regulating various cellular processes, including maintenance of the embryonic stem cell state, differentiation and metabolism. SetDB1 is best known as a chromatin mo...
ORGANISM(S): Mus musculus (Mouse) 
2026-08-20 | PXD074325 | Pride
Embryo Chep Epigenetics Conditional ko Escs Chromatin Setdb1 
TranscriptomicsSequencing of the non-ribosomal transcriptome allows the simultaneous identification of protein-coding and non-protein-coding RNAs
Deep Sequencing of protein-coding and non-protein-coding RNAs from mouse differentiated embryonic stem cells and 14.5dpc mouse fetal head Analysis of Ribominus RNA from mouse differentiated embryonic stem cells and 14.5dpc mouse fetal head There are no processed data files for GSM566806-GSM566811. ...
ORGANISM(S): Mus musculus 
2011-12-06 | E-GEOD-22959 | biostudies-arrayexpress
ProteomicsPolycomb Repressive Complex 2 Restricts Human Naive Pluripotent Stem Cell to Trophoblast Fate Induction
Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here, we apply multi-omics to comprehensively define the chromatin-associated proteome, ...
ORGANISM(S): Homo sapiens (Human) 
2022-05-06 | PXD028111 | Pride
Human Prc2 inhibition Chromatin Che 
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