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ProteomicsNuRD facilitates lineage decisions in human pluripotent cells
Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and, among the molecules that orchestrate these changes, chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. The NuRD complex is a highly conserved chromati...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2020-05-04 | PXD016967 | Pride
Human Ipsc Epiblast Mouse 
ProteomicsCharacterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression
Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part due to the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs tha...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-17 | PXD022697 | Pride
R-loop-interacting proteins Immunoprecipitation/mass spectrometry approach Rna-protein crosslinking 
ProteomicsInteractome of Eif4a2 in mouse embryonic stem cells
Cell fate transitions depend on balanced rewiring of transcription and translation programmes to enable ordered developmental progression. We identified a feedback loop between nonsense-mediated mRNA decay (NMD) and translation initiation, in which NMD controls the translation initiation factor Eif4...
ORGANISM(S): Mus musculus (Mouse) 
2022-03-09 | PXD019588 | Pride
Mouse embryonic stem cells Eif4a2 
ProteomicsChromatin immunoprecipitation of ectopic FLAG-tagged TCF7L1 followed by Mass Spectrome-try in H9-TCF7L1 Human Embryonic Stem Cells
TCF7L1 is a member of the T cell factor/Lymphoid enhancer factor (TCF/LEF) family of tran-scription factors that are part of the WNT/beta-CATENIN signaling pathway. TCF7L1 modulates transcription by interacting with other regulators on chromatin. TCF7L1 has been shown to be one of the key factors i...
ORGANISM(S): Homo sapiens (Human) 
2024-06-16 | PXD047582 | Pride
Mass spectrometry Human embryonic stem cells Immunoprecipitation Wnt/beta-catenin pathway Tcf7l1 
ProteomicsChd1 regulates repair of promoter-proximal DNA breaks to sustain hypertranscription in embryonic stem cells
Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation. The chromatin remodeler Chd1 binds to RNA Pol I and II genes and is required for hypertranscription in embryonic stem (ES) ce...
ORGANISM(S): Mus musculus (Mouse) 
2021-06-14 | PXD024604 | Pride
Mouse stem cell orbitrap immunoprecipitation mass spectrometry 
ProteomicsHuman non-small cell lung cancer cell line NCI-H661 DPPA2-4 rapid immunoprecipitation mass spectrometry (RIME, LC-MSMS)
To investigate DPPA2/4 bound proteins on chromatin we performed rapid immunoprecipitation mass spectrometry (RIME) following double crosslinking of chromatin in NCI-H661 non-small cell lung cancer cells clonal cell lines (Wild Type clones c51 & c52, DPPA2 knockout clones c41 & c42, DPPA4 knockout cl...
ORGANISM(S): Homo sapiens (Human) 
2026-03-31 | PXD070627 | Pride
Rime Dppa4 Non small cell lung cancer Ncih661 Dppa2 Human 
ProteomicsDynamic antagonism between key repressive pathways maintains the placental epigenome -1
DNA and Histone-3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb Repressive Complexes regulate the unmethylated CpG-rich promoters o...
ORGANISM(S): Mus musculus (Mouse) 
2023-01-27 | PXD039611 | Pride
Mouse trophoblast stem cells Epigenetic regulation Eed Polycomb 
ProteomicsIdentification of GLI-associated proteins by mass spectrometry
The Hedgehog signaling pathway is essential for the maintenance and response of several types of stem cells. To study the transcriptional response of stem cells to HH signaling, we searched for proteins binding to GLI proteins, the transcriptional effectors of the HH pathway in mouse embryonic stem ...
ORGANISM(S): Mus musculus (Mouse) 
2016-02-04 | PXD002494 | Pride
Nanog Embryonic stem cells Gli Hedgehog signaling 
ProteomicsIdentification of X-linked genes that drive sex differences in murine embryonic stem cells
Dosage imbalance of X-chromosomal genes contributes to sex differences, in particular during early development, when both X chromosomes are active in females. X-encoded inhibitors of the differentiation-promoting MAP kinase (MAPK) signalling pathway slow down development, increase levels of naive pl...
ORGANISM(S): Mus musculus (Mouse) 
2021-03-18 | PXD017875 | Pride
Klhl13 Sex differences Pluripotency Differentiation Mapk Mouse embryonic stem cells 
ProteomicsLIS1 RNA binding orchestartes the mechanosensitive properties of embryonic stem cells in AGO2 dependent and independent ways.
LIS1 immunoprecipitation in nuclear and cytoplasmic fractions of LIS1 Floxed/-, OE and WT embryonic stem cells. To identify AGO2 dependent and independent interactions LIS1 was immunoprecipitated in AGO1-4 knockout and doxycycline induced AGO2 mouse embryonic stem cells.
ORGANISM(S): Mus musculus (Mouse) 
2023-07-20 | PXD033150 | Pride
Oe Dox.ago2 Ago1-4 ko Nuclear and cytoplasmic fractions Flox/- Wt Mouse embyonic stem cells Lis1 ip 
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