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GenomicsCTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [ChIP-Seq]
In this experiment, we sought to identify how the distribution of CTCF, H3K27me3, H3K4me3, Pol II, H2AK119Ub1, EZH2 3 lines (WT, Δ5|6, Δ5|6:7|9)
ORGANISM(S): Mus musculus 
2015-02-26 | E-GEOD-60232 | biostudies-arrayexpress
GenomicsSIRT3 functions in the nucleus in the control of stress-related gene expression.
SIRT3 is a member of the Sir2 family of NAD+-dependent protein deacetylases that promotes longevity in many organisms. The processed, short form of SIRT3 is a well-established mitochondrial protein whose deacetylase activity regulates various metabolic processes. However, the presence of full-length...
ORGANISM(S): Homo sapiens 
2012-10-16 | E-GEOD-41000 | biostudies-arrayexpress
TranscriptomicsCTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [RNA-Seq]
In this experiment, we sought to analyze how the transcriptome of WT, Δ5|6, and Δ5|6:7|9 cells vary during differentiation of ESCs into cervical motor neurons 3 lines (WT, Δ5|6, Δ5|6:7|9)
ORGANISM(S): Mus musculus 
2015-02-26 | E-GEOD-60226 | biostudies-arrayexpress
TranscriptomicsCTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [4C-Seq]
In this experiment, we sought to analyze how the spatial organization of WT, Δ5|6, and Δ5|6:7|9 cells vary during differentiation of ESCs into cervical motor neurons 3 lines (WT, Δ5|6, Δ5|6:7|9)
ORGANISM(S): Mus musculus 
2015-02-26 | E-GEOD-60227 | biostudies-arrayexpress
GenomicsPCGF Homologs and RYBP Define Functionally Distinct PRC1 Family Complexes
The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, a...
ORGANISM(S): Homo sapiens 
2012-02-09 | E-GEOD-34774 | biostudies-arrayexpress
GenomicsChIP-seq for PRC2 components and H3K27me3 in E14 mouse embryonic stem cells
This experiment sought to determine the chromatin structure and PRC2 occupancy at the promoters of all genes in mouse ESCs ChIP-seq for EZH2, SUZ12, and H3K27me3 were performed on WT E14 cells in 2 biological replicates each. In addition H3K27me3 ChIP-seq was also performed on a clone of E14 cells e...
ORGANISM(S): Mus musculus 
2013-10-19 | E-GEOD-49431 | biostudies-arrayexpress
TranscriptomicsRNA seq in two lines of E14 mouse embryonic stem cells
This experiment was designed to obtain the polyA+ transcriptome in E14 ESCs PolyA+ RNA was extracted and purified from two separate clones of E14, which were treated as biological replicate
ORGANISM(S): Mus musculus 
2013-10-19 | E-GEOD-49434 | biostudies-arrayexpress
GenomicsJarid2 and PRC2, Partner in Regulating Gene Expression
The Polycomb Group proteins foster gene repression profiles required for proper development and unimpaired adulthood, and comprise the components of the PRC2 complex including the histone H3 lysine 27 (H3K27) methyltransferase Ezh2. How mammalian PRC2 accesses chromatin is unclear. We find that Jari...
ORGANISM(S): Mus musculus 
2010-01-01 | E-GEOD-19708 | biostudies-arrayexpress
TranscriptomicsThe C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation
The Carboxy-terminal domain (CTD) of RNA Polymerase II (RNAPII) in mammals undergoes extensive post-translational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the transcriptional co-...
ORGANISM(S): Homo sapiens 
2011-04-01 | E-GEOD-27315 | biostudies-arrayexpress
ProteomicsCTCF ChIP-MS from crosslinked chromatin in mouse embryonic stem cells (mESCs) and motor neurons (MNs)
To identify CTCF partners and co-localizing proteins from crosslinked chromatin in mESCs and MNs in endogenous conditions. The goal is to identify proteins within each sample with respect to wild-type control for each.
ORGANISM(S): Mus musculus (Mouse) 
2022-02-15 | PXD030543 | Pride
Mouse Crosslinked chromatin Ctcf chip-ms Ctcf partners Lc-ms/ms 
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