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MetabolomicsTFAM loss induces nuclear actin assembly upon mDia2 malonylation to promote liver cancer metastasis
The mechanisms underlying cancer metastasis remain poorly understood. Here, we report that TFAM deficiency rapidly and stably induced spontaneous lung metastasis in mice with liver cancer. Interestingly, unexpected polymerization of nuclear actin was observed in TFAM-knockdown HCC cells when cytoske...
2022-06-23 | MTBLS4307 | MetaboLights
TranscriptomicsMitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system
Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-17 | E-GEOD-34132 | biostudies-arrayexpress
ProteomicsShotgun analysis of nuclear proteins from mouse brain
Nuclei were isolated from the mouse brain. Proteins were extracted with addition of Bensonase and cleaned up by acetone precipitation. Proteis were resuspended in 50 mM ammonium bicarbonate and PPS Silent Surfactant. Samples were sonicated on ice to improve the solubility of proteins, then alkylated...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
MSV000079301 | MassIVE
TranscriptomicsRapid, high efficiency isolation of pancreatic ß-cells
The ability to isolate pure pancreatic ß-cells would greatly aid multiple areas of diabetes research. We developed an exendin-4-like neopeptide conjugate for the rapid purification and isolation of functional pancreatic ß-cells. By targeting the glucagon-like peptide-1 receptor, ß-cells were isolate...
ORGANISM(S): Mus musculus 
2015-09-04 | E-GEOD-64508 | biostudies-arrayexpress
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
TranscriptomicsTU-tagging: cell type specific RNA isolation from intact complex tissues
We show that the combination of spatially restricted uracil phosphoribosyltransferase (UPRT) expression with 4-thiouracil (4TU) delivery can be used to label and purify cell type specific RNA from intact complex tissues. This method is useful for isolating RNA from cell types that are difficult to i...
ORGANISM(S): Drosophila melanogaster 
2010-06-19 | E-GEOD-15445 | biostudies-arrayexpress
TranscriptomicsINTACT method for gene expression and chromatin profiling of individual cell types within a tissue
We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. Keywords: Chromatin affinity-purification ...
ORGANISM(S): Arabidopsis thaliana 
2010-06-13 | E-GEOD-19654 | biostudies-arrayexpress
ProteomicsFANS unfixed: isolation and proteomic analysis of mouse cell type-specific brain nuclei
Epigenetic-mediated gene regulation orchestrates brain cell-type gene expression programmes, and epigenetic dysregulation is a major driver of aging and disease-associated changes. Proteins that mediate gene regulation are mostly localised to the nucleus, however, nuclear-localised proteins are ofte...
ORGANISM(S): Mus musculus (Mouse) 
2024-08-09 | PXD053515 | Pride
Cell-type specific Proteomics Neurons Fans Microglia Epigenetics Oligodendrocytes 
ProteomicsSILAC proteomics on MG132-induced nuclear aggregates
H1299 cells were labelled either with light (Lys0/Arg0) or heavy (Lys8/Arg10) amino acids and were either unstressed (light), stressed (heavy) with MG132 (15hrs) or stressed with MG132 and allowed to recover for 8hrs (light). Equal number of unstressed and MG132 stressed cells or MG132 stressed cell...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD054637 | Pride
Nucleolus Nuclear inclusions Silac Proteasome Mg132 
TranscriptomicsInter- and intra- chromosomal interactions change on a global scale according to the metabolic regime employed by Saccharomyces cerevisiae
Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-17 | E-GEOD-33074 | biostudies-arrayexpress
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