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TranscriptomicsDynamic alterations of 3D chromatin structure during differentiation RNA-seq
Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked at long-range via positioning of loci to transcriptionally permissive (euchromatin) or repressive (heterochromatin) environments and at short-range by connecti...
ORGANISM(S): Mus musculus 
2019-08-27 | E-MTAB-2125 | biostudies-arrayexpress
GenomicsDynamic alterations of 3D chromatin structure during differentiation
Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked at long-range via positioning of loci to transcriptionally permissive (euchromatin) or repressive (heterochromatin) environments and at short-range by connecti...
ORGANISM(S): Mus musculus 
2019-08-27 | E-MTAB-2063 | biostudies-arrayexpress
GenomicsTCC in pluripotent and differentiated cells
Regulation of gene expression underlies the establishment and maintenance of cell identity. Chromatin structure and gene activity are linked. Recently CTCF anchored loops have been described as major features of chromatin organisation. However, the dynamics and role for these structures in differ...
ORGANISM(S): Mus musculus 
2018-11-08 | E-MTAB-4870 | biostudies-arrayexpress
TranscriptomicsGain of chromatin loops marks the exit from naïve pluripotency – in-situ Hi-C data
In-situ Hi-C data for mouse embryonic stem cells (ES cells, grown in the presence of FBS and LIF) and for NS cells.
ORGANISM(S): Mus musculus 
2018-11-08 | E-MTAB-6591 | biostudies-arrayexpress
TranscriptomicsBATSeq of ESC-FCS/ESC-2i/NSC
Single-cell polyadenylation site quantification 48 single cells each of murine embryonic stem cells maintained in FCS+LIF medium ("ESC"), embryonic stem cells maintained in serum free, 2i containing medium ("2i") and neural stem cells ("NSC") were sequenced by BATSeq, a...
ORGANISM(S): Mus musculus 
2015-06-09 | E-GEOD-60768 | biostudies-arrayexpress
GenomicsGain of chromatin loops marks the exit from naive pluripotency - ChIP seq for CTCF and Rad21
ChIP-seq to map the binding sites for CTCF and cohesin subunit Rad21 in the naive mES cells (46C cell line grown in the 2i/LIF condition) and in the neural stem cells (derived from the 46C ES cells using the mono-layer differentiation protocol, grown in the N2B27 medium these cells are Nestin+)....
ORGANISM(S): Mus musculus 
2018-11-08 | E-MTAB-5732 | biostudies-arrayexpress
GenomicsH3K4 tri-methylation provides an epigenetic signature of active enhancers
Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K...
ORGANISM(S): Mus musculus 
2014-03-07 | E-GEOD-55635 | biostudies-arrayexpress
GenomicsH3K27ac ChIP-seq from mouse embryonic stem cell and their derivative neural stem cells
H3K27ac ChIP-Seq experiment was performed to map and compare potential changes in elements of mouse embryonic stem cells and their derived neural stem cells
ORGANISM(S): Mus musculus 
2025-06-13 | E-MTAB-13560 | biostudies-arrayexpress
GenomicsCTCF ChIP-seq from mouse embryonic stem cell and their derivative neural stem cells
CTCF ChIP-Seq experiment was performed to map and compare potential changes of CTCF binding, in mouse embryonic stem cell and ES derived neural stem cells.
ORGANISM(S): Mus musculus 
2025-06-13 | E-MTAB-13562 | biostudies-arrayexpress
GenomicsTranscriptional landscape of Rag2 -/- thymocytes [Mnase-Seq]
We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene...
ORGANISM(S): Mus musculus 
2014-04-01 | E-GEOD-56360 | biostudies-arrayexpress
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