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ProteomicsZebrafish early embryos isolated nuclei and whole blastomeres LC-MSMS
Nuclear pore complex (NPC) structure and maturity changed during early development before MBT in zebrafish embryos. Aiming to further confirm the difference of NPCs among different stages during MZT, we first isolated nuclei from 32-cell and 512-cell stage embryos as most zygotic genes have not been...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2023-08-25 | PXD017896 | Pride
Whole blastomeres Lc-msms Isolated nuclei Zebrafish 
MetabolomicsOperation of a TCA cycle subnetwork in the mammalian nucleus

Nucleic acid and histone modifications critically depend on tricarboxylic acid (TCA) cycle for substrates and co-factors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to operate in mitochondria. Here, we show that a part of the...

2022-06-15 | MTBLS2235 | MetaboLights
TranscriptomicsSingle-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells
Syncytial skeletal muscle cells contain hundreds of nuclei in a shared cytoplasm. Using single nucleus RNA-sequencing (snRNAseq) of isolated nuclei from muscle fibers, we investigated nuclear heterogeneity and transcriptional dynamics in uninjured and regenerating muscle.
ORGANISM(S): Mus musculus 
2020-10-07 | E-MTAB-8623 | biostudies-arrayexpress
ProteomicsHistone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei
Cells organize their actions partly through tightly controlled protein-protein interactions – collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the interactome of intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links ...
ORGANISM(S): Homo sapiens (Human) 
2018-07-23 | PXD007513 | Pride
Crosslinking mass spectrometry Histone interaction network – ptm interplay Nuclear interactome Histone variant specific interactions Nuclear protein-protein interactions 
TranscriptomicsSingle nuclei RNA-seq from adult mouse Hippocampus
We report RNA-seq of single nuclei isolated from the adult C57BL/6 male mouse Hippocampus region. Majority of the nuclei were isolated from 12 weeks old mice (4 different animal), with an additional set of nuclei from 3 months and 2 years old animals. In addition a set of GFP labeled nuclei driven b...
ORGANISM(S): Mus musculus 
2016-08-16 | E-GEOD-85721 | biostudies-arrayexpress
TranscriptomicsGlobal analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any or...
ORGANISM(S): Arabidopsis thaliana 
2014-12-16 | E-GEOD-58974 | biostudies-arrayexpress
GenomicsRNA profile of nuclei isolated from neurons coexpressing VAChT and VGlut or VAChT and VGAT
RNA profile of nuclei isolated from neurons coexpressing VAChT and VGlut or VAChT and VGAT
PRJNA916511 | ENA
UnknownIsolated nuclei stiffen in response to low intensity vibration.
Not available
S-EPMC7590198 | biostudies-literature
GenomicsSubsets of visceral adipose tissue nuclei with discrete levels of 5-hydroxymethylcytosine
We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We devel...
ORGANISM(S): Sus scrofa 
2016-07-20 | E-GEOD-73684 | biostudies-arrayexpress
GenomicsSingle nucleus RNAseq of midbrain dopaminergic neuronal nuclei isolated by FACS
Single nucleus RNAseq of midbrain dopaminergic neuronal nuclei isolated by FACS
PRJNA922521 | ENA
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