Browse
Submit Data
Databases
API
Help

Dataset Information

169 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MitoSILAC - Comparison of control and promoter mutant mitochondrial proteomes.

ABSTRACT: Comparison of control and promoter mutant mitochondrial proteomes.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Fibroblast

DISEASE(S): Kidney Disease

SUBMITTER: Yagnesh Umrania

LAB HEAD: Patrick Maxwell

PROVIDER: PXD004809 | Pride | 2017-03-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SH_mitoA_1_281114_run1.raw	Raw
	SH_mitoA_2_281114_run1.raw	Raw
	SH_mitoA_3_281114_run1.raw	Raw
	SH_mitoA_4_281114_run1.raw	Raw
	SH_mitoA_5_281114_run1.raw	Raw

Items per page:

1 - 5 of 33

Similar Datasets

USP7 protects TFEB from proteasome-mediated degradation

Project description:The transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and autophagy. We identify a distinct nuclear interactome of TFEB, with USP7 emerging as a key post-translational modulator of TFEB. Genetic depletion and inhibition of USP7 reveal its critical role in preserving TFEB stability within both nuclear and cytoplasmic compartments. Specifically, USP7 is identified as the deubiquitinase responsible for removing the K48-linked polyubiquitination signal from TFEB at lysine residues K116, K264, and K274, thereby preventing its proteasomal degradation. Functional assays demonstrate the involvement of USP7 in preserving TFEB-mediated transcriptional responses to nutrient deprivation, while also modulating autophagy flux and lysosome biogenesis. As USP7 is a deubiquitinase that protects TFEB from proteasomal degradation, these findings provide the foundation for therapeutic targeting of the USP7-TFEB axis in conditions characterized by TFEB dysregulation and metabolic abnormalities, particularly in certain cancers.

2024-09-17 | PXD055937 | Pride

RNA-seq of nonstenotic and stenotic areas of patients with Crohn’s disease

Project description:Fibrostenotic disease is a common complication in Crohn’s disease (CD). We performed bulk RNA sequencing (n=16) of paired intestinal biopsies taken from nonstenotic and stenotic areas of patients with CD (n=8).

2023-04-26 | E-MTAB-12788 | biostudies-arrayexpress

The hTERT-RPE1 secretome after TLR3 stimulation

Project description:RPE cells perform a number of support functions in the inner eye including the secretion of signalling molecules and the maintenance of the immune privileged environment through communication with the immune system (Detrick and Hooks, 2010). Previous reports have demonstrated that RPE cells express a number of TLRs including the viral RNA receptor TLR3. To determine the complete secretory response of RPE cells downstream of poly(I:C) stimulation, we analysed conditioned medium from unstimulated or poly(I:C)-stimulated RPE cells using quantitative SILAC mass spectrometry.

2020-06-16 | PXD019445 | Pride

The pluripotent genome in three dimensions is shaped around pluripotency factors

Project description:It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells (PSCs) such as embryonic stem cells (ESCs) were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types. Here, we applied 4C technology and combined ChIP-seq with Hi-C data to demonstrate that inactive chromatin is unusually disorganized in PSC nuclei. We show that gene promoters engage in contacts between topological domains in a largely tissue-independent manner while enhancers have a more tissue-restricted interaction profile. Most strikingly, genomic clusters of pluripotency factor binding sites find each other very efficiently, in a manner that is strictly PSC-specific, dependent on the presence of Oct4 and Nanog protein and inducible upon artificial recruitment of Nanog to a selected chromosomal site. We conclude that pluripotent stem cells have a unique higher-order genome structure shaped by pluripotency factors. We speculate that this interactome enhances the robustness of the pluripotent state. 4C-seq was performed on a range of viewpoints in pluripotent (2x ESC, iPSC) and differentiated (neural precursor cells and astrocytes) cell lines.

2013-07-24 | E-GEOD-37275 | biostudies-arrayexpress

Introducing synthetic thermostable RNase inhibitors in single-cell RNA-seq (Bulk RNA-seq libraries)

Project description:Single-cell RNA-sequencing (scRNAseq) is revolutionizing biomedicine, propelled by advances in methodology, ease of use, and cost reduction of library preparation. Over the past decade, there have been remarkable technical improvements in most aspects of single-cell transcriptomics. Yet, there has been little to no progress in advancing RNase inhibition despite that maintained RNA integrity is critical during cell collection, storage, and cDNA library generation. Here, we demonstrate that a synthetic thermostable RNase inhibitor yield single-cell libraries of equal or superior quality compared to ubiquitously used protein-based recombinant RNase inhibitors (RRIs). Importantly, the synthetic RNase inhibitor provide additional unique improvements in reproducibility and throughput, enable new experimental workflows including heat cycles, and can reduce the need for dry-ice transports. In summary, replacing RRIs represents a substantial advancement in the field of single-cell transcriptomics.

2024-07-26 | E-MTAB-13899 | biostudies-arrayexpress

Transcription profiling of human MCF7 cells infected with adenovirus expressing c-Myb, v-Myb or the hybrid construct, 3MutC

Project description:The transcriptional activities of c-Myb and its oncogenic variant v-Myb were compared by expressing them in human MCF7 cells using recombinant adenovirus vectors. A hybrid construct, 3Mutc, which is a variant of c-Myb harboring three v-Myb-derived DNA binding domain mutations was also analyzed. All the samples were compared to cells infected with a control adenovirus. The results showed that v-Myb, which differs from c-Myb only by N- and C-terminal deletions and eleven amino acid substitutions, has a qualitatively different transcriptional activity. Experiment Overall Design: 2 replicates of each type were analyzed. Replicates were performed independently, more than a week apart.

2007-12-12 | E-GEOD-2815 | biostudies-arrayexpress

Constitutional Trisomy 8 Mosaicism as a Model for Epigenetic Studies of Aneuploidy

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-12-01 | E-GEOD-40321 | biostudies-arrayexpress

RNA-Seq analysis of human osteoarthritic intact cartilage following total knee replacement

Project description:Large scale RNA-Seq analysis was performed to investigate the transcriptomic response to osteoarthritis in cartilage and investigate potential subgroups of patients. Data were collected from intact knee cartilage (posterior lateral condyle) from at total of 60 patients with osteoarthritis (OA) following total knee replacement and 10 control non-OA patients following amputation.

2017-12-13 | E-MTAB-6266 | biostudies-arrayexpress

Constitutional Trisomy 8 Mosaicism as a Model for Epigenetic Studies of Aneuploidy (DNA methylation)

Project description:To increase our understanding of epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient. We profiled gene and miRNA expression as well as genome-wide and promoter specific DNA methylation and hydroxymethylation patterns in trisomic and disomic fibroblasts, using microarrays and methylated DNA immunoprecipitation. comparison of trisomy 8 cells with disomic as well as reference fibroblasts

2012-12-01 | E-GEOD-40317 | biostudies-arrayexpress

Transcription profiling of human monocytes infected with adenovirus expressing either c-Myb or v-Myb

Project description:The transcriptional activities of c-Myb and its oncogenic variant v-Myb were compared by expressing them in primary human monocytes using recombinant adenovirus vectors. All the samples were compared to cells infected with a control adenovirus expressing only GFP. The results showed that v-Myb, which differs from c-Myb only by N- and C-terminal deletions and eleven amino acid substitutions, has a qualitatively different transcriptional activity. Experiment Overall Design: 2 replicates of each type were analyzed. Replicates were performed independently, more than a week apart.

2007-12-12 | E-GEOD-2816 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data