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Metabolomics1H NMR metabolite monitoring during the differentiation of human induced pluripotent stem cells provides new insights into the molecular events that regulate embryonic chondrogenesis
The integration of cell metabolism with signalling pathways, transcription factor networks and epigenetic mediators is critical in coordinating molecular and cellular events during embryogenesis. Induced pluripotent stem cells (IPSCs) are an established model for embryogenesis, germ layer specificat...
2023-05-24 | MTBLS4854 | MetaboLights
TranscriptomicsBiochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA
Biochemical fractionation of HEK293 nuclei and RNA-seq of chromatin-associated and soluble-nuclear RNA. Nuclei from three biological replicates were isolated by detergent lysis, fractionated, then three chromatin and three soluble RNA samples were converted to cDNA using Illumina TruSeq stranded pro...
ORGANISM(S): Homo sapiens 
2015-03-04 | E-GEOD-66478 | biostudies-arrayexpress
ProteomicsDifferential nuclear import sets the timing of protein access to the embryonic genome
During early embryonic cell divisions, the total nuclear volume doubles with each cycle. At a critical volume ratio between the nucleus and cytoplasm, embryos start transcribing their genome in a reproducible and sequential manner. However, the underlying molecular mechanism for these well-timed eve...
ORGANISM(S): Xenopus laevis (African clawed frog) 
2022-08-30 | PXD036403 | Pride
Multiplexed quantitative proteomics Lc-ms Xenopus embryo Nucleocytoplasmic partitioning Zygotic gene activation Early embryogenesis Nuclear import 
ProteomicsDifferential nuclear import sets the timing of protein access to the embryonic genome
During early embryonic cell divisions, the total nuclear volume doubles with each cycle. At a critical volume ratio between the nucleus and cytoplasm, embryos start transcribing their genome in a reproducible and sequential manner. However, the underlying molecular mechanism for these well-timed eve...
ORGANISM(S): Xenopus laevis (African clawed frog) 
2022-08-30 | PXD028069 | Pride
Multiplexed quantitative proteomics Lc-ms Xenopus embryo Nucleocytoplasmic partitioning Zygotic gene activation Early embryogenesis Nuclear import 
TranscriptomicsGeminin-regulated genes during neural fate acquisition of mouse embryonic stem cells
Formation of the complex vertebrate nervous system begins when pluripotent cells of the early embryo are directed to acquire a neural fate. Although cell intrinsic controls play an important role in this process, the molecular nature of this regulation is not well defined. Here we assessed the rol...
ORGANISM(S): Mus musculus 
2011-03-18 | E-GEOD-25737 | biostudies-arrayexpress
ProteomicsAnalysis of nuclear extracts from E14 mouse embryonic stem cells
Generated nuclear extracts from embryonic stems cells were compared to cytosolic extracts using shotgun proteomics and labe-free-quantitation.
ORGANISM(S): Mus musculus (Mouse) 
2025-01-02 | PXD041753 | Pride
Nuclear extracts Embryonic stem cells Label-free quantitation 
TranscriptomicsConnecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
MicroRNAs (miRNAs) are crucial for normal embryonic stem (ES) cell self-renewal and cellular differentiation, but how miRNA gene expression is controlled by the key transcriptional regulators of ES cells has not been established. We describe here a new map of the transcriptional regulatory circuitr...
ORGANISM(S): Mus musculus 
2008-07-29 | E-GEOD-11724 | biostudies-arrayexpress
TranscriptomicsWhole Cell Extract for Mouse Embryonic Fibroblasts
Mouse embryonic fibroblasts (MEFs) are an example of an early differentiated cell type. The whole cell extract was prepared in order to have background information for additional ChIP-Seq experiments in MEFs. The WCE data is a useful dataset that can be used as a background for many different analy...
ORGANISM(S): Mus musculus 
2010-06-15 | E-GEOD-22320 | biostudies-arrayexpress
ProteomicsM1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity
In order to identify more gypsy insulator interactors, we performed immunoaffinity purification of Drosophila embryonic nuclear extracts using antibodies specific for CP190 and analyzed the eluates using quantitative mass spectrometry.
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2021-06-07 | PXD026493 | Pride
Mass spectrometry Drosophila Cp190 Embryonic nuclear extract 
TranscriptomicsXenopus M-phase extract treated induced pluripotent stem cells
Transfer of somatic cell nuclei to enucleated eggs or ectopic expression of specific transcription factors are two different reprogramming strategies used to generate pluripotent cells from differentiated cells. However, they are poorly efficient and other unknown factors might be required to increa...
ORGANISM(S): Mus musculus 
2011-11-21 | E-GEOD-31691 | biostudies-arrayexpress
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