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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
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 
TranscriptomicsTissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.
Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method t...
ORGANISM(S): Caenorhabditis elegans 
2011-12-05 | E-GEOD-31602 | 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
ProteomicsA multi-omics approach to liver diseases: integration of Single Nuclei Transcriptomics with Proteomics and Hi-Cap Bulk Data in human liver
Abstract The liver is the largest solid organ and a primary metabolic hub. In recent years, intact cell nuclei were used to perform single-nuclei RNA-seq (snRNA-seq) for tissues difficult to dissociate and for flash-frozen archived tissue samples to discover unknown and rare cell sub-populations. In...
ORGANISM(S): Homo sapiens (Human) 
2020-12-21 | PXD017610 | Pride
Human liver single nuclei lcms 
TranscriptomicsAnalysis of Caenorhabditis elegans intestinal gene expression and alternative polyadenylation using fluorescence-activated nuclei sorting (FANS) and 3' end deep sequencing (3'end-seq)
Caenorhabditis elegans is a major eukaryotic experimental system employed to unravel a broad range of cellular and biological processes. Despite the many advantages of C. elegans, biochemical approaches to study tissue-specific gene expression in postembryonic stages are challenging. Here we report ...
ORGANISM(S): Caenorhabditis elegans 
2011-12-01 | E-GEOD-32165 | biostudies-arrayexpress
GenomicsHuman cortical nuclei RNAseq
Human cortical nuclei RNAseq
PRJNA631228 | ENA
GenomicsTranscriptomic atlas of thalamic nuclei
Transcriptomic atlas of thalamic nuclei
PRJNA552996 | ENA
TranscriptomicsSingle nuclei RNA-seq of spinal cord from Eif2b5[R191H] mice
The integrated stress response (ISR) is a conserved signaling pathway triggered by a variety of insults that include ER stress, mitochondrial stress, amino acid deprivation, and viral infection. The essential stress sensor and key effector of this pathway is eIF2B, and loss-of-function mutations in ...
ORGANISM(S): Mus musculus 
2025-07-10 | E-MTAB-15295 | biostudies-arrayexpress
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