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TranscriptomicsMLL2 facilitates long-range gene regulation through LINE1 elements [scRNA-seq]
Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 deposition at bivalent promoters, which has been proposed to facilitate the induction of major develo...
ORGANISM(S): Mus musculus 
2026-07-12 | E-MTAB-17228 | biostudies-arrayexpress
TranscriptomicsMLL2 facilitates long-range gene regulation through LINE1 elements [Micro-C]
Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 deposition at bivalent promoters, which has been proposed to facilitate the induction of major develo...
ORGANISM(S): Mus musculus 
2025-10-23 | E-MTAB-15688 | biostudies-arrayexpress
GenomicsRegulation of nucleosome architecture and factor binding revealed by nuclease footprinting of the ESC genome
Functional interactions between gene regulatory factors and chromatin architecture have been difficult to directly assess. Here, we use micrococcal nuclease (MNase) footprinting to probe the functions of two chromatin remodeling complexes. By simultaneously quantifying alterations in small MNase foo...
ORGANISM(S): Mus musculus 
2015-08-27 | E-GEOD-68400 | biostudies-arrayexpress
TranscriptomicsTimed induction of 50 transcription factors in ES cells reveals a common mechanism to initiate differentiations
To decipher the structure and behaviors of the transcription factor (TF) network, we created 50 permanent mouse ES cell lines, in each of which one of the 50 transcription factors tagged with FLAG, is inserted into the doxycycline (dox)-repressible ROSA26 locus. Expression profiling reveals Cdx2 as ...
ORGANISM(S): Mus musculus 
2009-10-01 | E-GEOD-14559 | biostudies-arrayexpress
TranscriptomicsSuv39h-dependent H3K9me3 represses intact retrotransposons in mouse embryonic stem cells
Heterochromatin is required to restrict aberrant expression of retrotransposons, but it remains poorly defined due to the underlying repeat-rich sequences. We dissected Suv39h-dependent histone H3 lysine 9 trimethylation (H3K9me3) by genome-wide ChIP-sequencing in mouse embryonic stem cells (ESCs). ...
ORGANISM(S): Mus musculus 
2014-06-26 | E-GEOD-57092 | biostudies-arrayexpress
TranscriptomicsSuppression of pervasive noncoding transcription in embryonic stem cells by esBAF
Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, most noncoding RNA (ncRNA) is rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, ...
ORGANISM(S): Mus musculus 
2015-02-12 | E-GEOD-57170 | biostudies-arrayexpress
GenomicsPromoter capture mESC and fetal liver
Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in HiC libraries from mouse ESC and E14.5 fetal liver. Pl...
ORGANISM(S): Mus musculus 
2015-02-01 | E-MTAB-2414 | biostudies-arrayexpress
TranscriptomicsRelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (Promoter)
A study to define the binding loci of RelA-containing NF-kappaB dimers in a human myometrial smooth muscle cell line after exposure to TNF. Monolayers of PHM1-31 cells were exposed to TNF (10ng/ml) for 1 hour or left unstimulated. The Chromatin immunoprecipitation (ChIP) assay was performed to recov...
ORGANISM(S): Homo sapiens 
2015-03-31 | E-GEOD-65690 | biostudies-arrayexpress
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