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GenomicsGenome-wide H3K9 acetylation state before and after VPA treatment
Genome-wide maps of the H3K9 acetylation state in embryonic stem cells (ESCs) before and after treatment with low levels of the histone deacetylase (HDAC) inhibitor valproic acid (VPA). ChIP-seq for 3 samples: untreated E14 cells, cells treated with VPA for 4 hrs and cells treated with VPA for 16 hr...
ORGANISM(S): Mus musculus 
2011-09-17 | E-GEOD-24211 | biostudies-arrayexpress
TranscriptomicsGenome-wide non-polyadenylated transcription in differentiating mouse embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation
The transcriptional landscape in embryonic stem cells (ESCs) and during ESC differentiation has received considerable attention in recent years, but reports have so far been confined to the polyadenylated fraction of RNA, while the non-polyadenylated (NPA) fraction remained largely unexplored. Notwi...
ORGANISM(S): Mus musculus 
2013-04-17 | E-GEOD-37338 | biostudies-arrayexpress
TranscriptomicsHP1 is involved in regulating the global impact of DNA methylation on alternative splicing
The global impact of DNA methylation on alternative splicing is largely unknown. Using a genome-wide approach in wild-type and methylation-deficient embryonic stem cells, we found that DNA methylation can act both as an enhancer and as a silencer of splicing, and affects the splicing of more than 20...
ORGANISM(S): Mus musculus 
2015-03-08 | E-GEOD-64910 | biostudies-arrayexpress
TranscriptomicsGene expression and H3K9ac genome-wide maps following HDAC inhibition in mouse ES cells
This SuperSeries is composed of the following subset Series: GSE23956: Gene expression profiles of E14 ESCs treated with low levels of HDAC inhibitors for 16 hrs GSE23957: Gene expression profiles of E14 ESCs treated with low levels of the HDAC inhibitor VPA for 4 hrs GSE24211: Genome-wide H3K9 acet...
ORGANISM(S): Mus musculus 
2011-09-16 | E-GEOD-23958 | biostudies-arrayexpress
TranscriptomicsHP1? has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [expression]
We used microarrays to identify the gene expression changes in Cbx1-/- (HP1beta) knockout embryonic stem cells (ESCs) and Cbx5-/- (HP1alpha) knockout ESCs compared to WT ESCs and in embryoid bodies (EBs) differentiated from those three ESC types. ESCs were grown and the pluripotent SSEA1-positive ce...
ORGANISM(S): Mus musculus 
2015-08-02 | E-GEOD-65121 | biostudies-arrayexpress
GenomicsSF3B1 association with chromatin determines splicing outcomes
Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. Part of the explanation probably lies in differences in chromatin organization between exons and introns. Pro...
ORGANISM(S): Homo sapiens 
2015-04-22 | E-GEOD-65644 | biostudies-arrayexpress
TranscriptomicsGene expression profiles of E14 ESCs treated with low levels of HDAC inhibitors for 16 hrs
Gene expression profiles of E14 embryonic stem cells (ESCs) before and after treatment with low levels of the histone deacetylase (HDAC) inhibitors valproic acid (VPA) and sodium butyrate (NaBu). E14 cells were treated with VPA or NaBu for 16 hrs in duplicates. Cells were harvested along with untrea...
ORGANISM(S): Mus musculus 
2011-09-16 | E-GEOD-23956 | biostudies-arrayexpress
TranscriptomicsGene expression profiles of E14 ESCs treated with low levels of the HDAC inhibitor VPA for 4 hrs
Gene expression profiles of E14 embryonic stem cells (ESCs) before and after treatment with low levels of the histone deacetylase (HDAC) inhibitor valproic acid (VPA). E14 cells were treated with valproic acid for 4 hrs in duplicates. Cells were harvested along with untreated control E14 cells. RNA ...
ORGANISM(S): Mus musculus 
2011-09-16 | E-GEOD-23957 | biostudies-arrayexpress
TranscriptomicsExpression data from Smarcd1 knockdown R1 embryonic stem cells
We used microarrays to identify the gene expression changes after Smarcd1 knockdown in ESCs and 4 day RA differentiated ESCs Actively growing ESCs and 4d RA differentiated ESCs were harvested and RNA was extracted immediately.
ORGANISM(S): Mus musculus 
2015-03-01 | E-GEOD-65089 | biostudies-arrayexpress
GenomicsDistribution of total histone variants H3.1 and H3.3 in pluripotent mouse embryonic stem cells (mESCs) and in vitro differentiated neuronal precursor cells (NPCs)
We profiled the enrichment of the replicative H3.1 and non-replicative H3.3 histone variants using the SNAP-seq assay previously developed in the team (Gatto et al., 2022, Forest et al., 2023). We used KH2 mouse embryonic stem cells (mESCs) bearing doxycycline-inducible H3.1/H3.3-SNAP, which were ex...
ORGANISM(S): Mus musculus 
2025-04-24 | E-MTAB-14240 | biostudies-arrayexpress
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