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ProteomicsYME1L1 Degrades Mitochondria Protein Import Complex TIMM17A and TIMM23 Subunits and Protects Cells upon Import Plugging
Mitochondrial protein import through the outer and inner membranes is key to mitochondrial biogenesis. Recent studies have explored how cells respond when import is impaired by a variety of different insults. Here, we developed a mammalian import blocking system using dihydrofolate reductase (DHFR) ...
ORGANISM(S): Human 
2024-10-24 | MSV000096201 | MassIVE
TranscriptomicsRNA-seq of CD8 single positive thymocytes from WT and Rela fx/fx CD4Cre Nfkb1KO RelKO mice.
Gene expression by CD8 thymocytes was compared between cells from WT mice, and cell from mice with gremlin deletions of cRel and Nfkb1, and a T cell specific deletion of Rel using CD4 Cre.
ORGANISM(S): Mus musculus 
2019-08-23 | E-MTAB-7470 | biostudies-arrayexpress
Metabolomics13C glucose labelling studies using 2D NMR is a useful tool for determining ex vivo whole organ metabolism during hypothermic machine perfusion of kidneys
Background: The aim of this study is to determine the feasibility of using Nuclear Magnetic Resonance (NMR) tracer studies (13C-enriched glucose) to detect ex vivo de novo metabolism in the perfusion fluid and cortical tissue of porcine kidneys during hypothermic machine perfusion (HMP). Methods: Po...
2017-10-16 | MTBLS367 | MetaboLights
TranscriptomicsHuman uterine Natural Killer cells regulate differentiation of extravillous trophoblast early in pregnancy - scRNA-seq data
We used trophoblast organoids differentiating to extravillous trophoblast (EVT) to study the effects of key cytokines secreted by uterine Natural Killer (uNK) cells on EVT behaviour. Specifically, we exposed the organoids to four uNK-derived cytokines (CSF1, CSF2, XCL1, CCL5) and collected cells at ...
ORGANISM(S): Homo sapiens 
2024-01-10 | E-MTAB-13382 | biostudies-arrayexpress
TranscriptomicsRIP-chip analysis of the C. elegans PUF protein FBF
The PUF family of RNA binding proteins has a conserved role in maintaining stem cell self-renewal. FBF is a C. elegans PUF that is required to maintain germline stem cells (GSCs). To understand how FBF controls GSCs, we sought to identify is target mRNAs. Briefly, we immunoprecipitated FBF-mRNA c...
ORGANISM(S): Caenorhabditis elegans 
2010-02-21 | E-GEOD-19922 | biostudies-arrayexpress
ProteomicsUSP16 Regulates Mitochondrial Function by Deubiquitinating TOM40, A Core Component of the Translocase in Mitochondrial Outer Membrane_AP-MS
The ubiquitin-specific protease 16 (USP16), initially identified as a histone H2A-specific deubiquitinase. However, whether endogenous USP16 localizes to mitochondria and, if so, how it regulates mitochondrial function remain unclear. Therefore, this study focused on USP16, systematically investigat...
ORGANISM(S): Homo Sapiens 
2025-07-05 | PXD065823 |
TranscriptomicsPotential biomarker genes for crowding stress in rainbow trout Oncorhynchus mykiss
Stocking density is considered as a key factor determining the productivity of fish aquaculture systems. The transcriptomic response to crowding stress is, however, still poorly investigated. We aimed at the identification of potential biomarker genes via microarray analyses to get insight into mole...
ORGANISM(S): Oncorhynchus mykiss 
2015-10-24 | E-GEOD-74332 | biostudies-arrayexpress
ProteomicsSubstrate Identification Using a Chemical Genetics Approach Reveals a Role for PARP-7-Mediated MARylation in Controlling Microtubule Stability in Ovarian Cancer Cells
To identify the ADPRylated substrates that underlie PARP-7-mediated ovarian cancer cell phenotypes, we developed an NAD+ analog-sensitive approach for PARP-7 comprising a PARP-7 NAD+ binding pocket mutant (S563G) paired with the NAD+ analog 8-Bu(3-yne)T-NAD+. When coupled with mass spectrometry, th...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-12-17 | MSV000086611 | MassIVE
TranscriptomicsRNA-seq of mice TRAF2/Casp-8LPC-KO tumors
This model was used to study the relationship between NF-kB and PCD regulation and generated mice with combined conditional ablation of Traf2 and Caspase-8 (TRAF2/Casp-8LPC-KO) in order to block apoptosis and specifically study the role of necroptosis in Traf2-deficient hepatocytes in vivo.
ORGANISM(S): Mus musculus 
2019-05-31 | E-MTAB-4598 | biostudies-arrayexpress
TranscriptomicsAn Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks
The specialisation of mammalian cells in time and space requires genes associated with specific pathways and functions to be co-ordinately expressed. Here we have combined a large number of publically available microarray datasets (745 samples, from over 100 separate studies) derived from human pr...
ORGANISM(S): Homo sapiens 
2013-08-16 | E-GEOD-49910 | biostudies-arrayexpress
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