Proteome-wide identification of Hsc70 clients in autophagy altered K-Ras G12V MEFs
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus Musculus (mouse)
SUBMITTER: Dr. Amit Kumar
PROVIDER: PXD029905 | JPOST Repository | Fri Nov 25 00:00:00 GMT 2022
REPOSITORIES: jPOST
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Individual.pdStudy | Other | |||
| Individual.pdStudy.bak | Other | |||
| S1_1.msf | Msf | |||
| S1_1.msfView | Msf | |||
| S1_1.pdResult | Other |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:We identified protein-protein interactions and chromatin binding sites for two isforms of BRD1 (BRD1-S and BRD1-L) using Co-IP MS/MS and ChIP-seq. BRD1 isoforms were cloned, epitope-tagged (pcDNA 6 V5-His6, Lifetechnologies) and stably expressed in HEK293T cells. Chromatin immunoprecipitations were performed using anti V5-antibody conjugated agarose beads (Sigma-Aldrich) and anti HA antibody conjugated agarose beads (Sigma-Aldrich) as controls
2015-10-29 | E-GEOD-62811 | biostudies-arrayexpress
Project description:Autophagy plays an important role in physiology and tumorigenesis. We and others have demonstrated that Ha-ras overexpression induces autophagy in NIH3T3 cells. Autophagic machinery is regulated by a family of autophagy associated genes (Atg). The inducible Ha-ras oncogene was introduced into mouse embryo fibroblast Atg5 wild type [MEF-Atg5(+/+)] and Atg5 knock-out [MEF-Atg5(-/-)] cells and the stable cell lines MR and M5R were established, respectively. Our results showed that M5R cell induced larger tumor formation compared with MR cells while these two cell lines were subcutaneously injected into SCID mice under Ha-ras overexpression conditions. It indicates that Atg5 is involved in the suppression of Ras-related tumor formation. MicroRNA (miRNA), approximately 22 nucleotide of non-coding RNA, regulates transcription and translation of the target genes and is involved in cell differentiation and tumorigenesis. A miRNA microarray (932 probes) screening was conducted to identify the autophagy-tumorigenesis-related miRNAs. Among the significant genes, miR-224 was highly expressed in autophagy deficient cell and it induced tumors. Overexpression miR-224 enhanced the activity of migration and invasion in vitro and tumor formation in vivo. In conclusion, this is the first report to demonstrate that autophagy suppresses tumor formation through down-regulation of microRNA in this case miR-224. MR and M5R cell lines were treated with IPTG for 48 hr. In addition, these cell lines were subcutaneously injected into mice to induce tumor formation. The RNA samples were extracted from above cell lines and tumors. In this research, BEL/ITRI 15K V1.0 miRNA microarray chips were used to evaluate the miRNA expression profile.
2012-06-25 | E-GEOD-38911 | biostudies-arrayexpress
Project description:Results from co-immunoprecipitation (co-IP)-MS analysis of VIPP-YFP bait, expressed in Arabidopsis thaliana via1 mutant line. GFP-Trap magnetic agarose beads were used for co-IP. Co-precipitated peptides were digested on the beads and analyzed by liquid chromatography-mass spectrometry (LC-MS). The MS data were processed using the Philosopher toolkit, with MSFragger as the search engine, followed by IonQuant. SAINTexpress software was used to score potential interactions between the observed proteins (potential prey) and the bait protein. It is recommended to use .raw files for reanalysis.
| MSV000099086 | MassIVE
Project description:Autophagy plays an important role in physiology and tumorigenesis. We and others have demonstrated that Ha-ras overexpression induces autophagy in NIH3T3 cells. Autophagic machinery is regulated by a family of autophagy associated genes (Atg). The inducible Ha-ras oncogene was introduced into mouse embryo fibroblast Atg5 wild type [MEF-Atg5(+/+)] and Atg5 knock-out [MEF-Atg5(-/-)] cells and the stable cell lines MR and M5R were established, respectively. Our results showed that M5R cell induced larger tumor formation compared with MR cells while these two cell lines were subcutaneously injected into SCID mice under Ha-ras overexpression conditions. It indicates that Atg5 is involved in the suppression of Ras-related tumor formation. MicroRNA (miRNA), approximately 22 nucleotide of non-coding RNA, regulates transcription and translation of the target genes and is involved in cell differentiation and tumorigenesis. A miRNA microarray (932 probes) screening was conducted to identify the autophagy-tumorigenesis-related miRNAs. Among the significant genes, miR-224 was highly expressed in autophagy deficient cell and it induced tumors. Overexpression miR-224 enhanced the activity of migration and invasion in vitro and tumor formation in vivo. In conclusion, this is the first report to demonstrate that autophagy suppresses tumor formation through down-regulation of microRNA in this case miR-224.
2012-06-26 | GSE38911 | GEO
Project description:In order to identify the comprehensive composition of Arabidopsis mitochondrial ribosome proteins, a strategy based on complementary approaches was used. Classical biochemical purification of ribosomes was combined with the immunoprecipitation of mitoribosomes using a specific Arabidopsis mitoribosome protein as a bait and quantitative proteomics. The immuno-purifications (IP) of the mitoribosome were performed on purified mitochondria from rPPR1-HA plant line (flowers as starting material). IPs were performed performed in different conditions (i.e. with 100, 400 or 600 mM KCl at the IP washing step or 800mM all along the IP). For each condition, experiments were performed in triplicates and IP proteins were identified by quantitative nano LC-ESI-MS/MS. Classic biochemical purification of mitochondrial monosomes (i.e. free ribosomes) was also performed. Starting from purified wild-type Arabidopsis mitochondria (cell culture as starting material), ribosomes were separated on high resolution 10-30% continuous sucrose gradients and mitoribosome containing fractions were analyzed by quantitative nano LC-ESI-MS/MS.
2018-12-14 | PXD010324 | Pride
Project description:DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively
2010-03-25 | GSE18535 | GEO
Project description:Analysis of ethylene mutant (eto1-4) genome expression profile altered by ethylene antagonists. Results uncovered a significant number of genes that were co-regulated by the ethylene antagonists which may contribution on phenotype difference between WT and eto1-4. WT (Col-0) or ethylene mutant (eto1-4) were etiolated growth 3-day on 0.5x MS medium as control. Ethylene mutant (eto1-4) etiolated growth 3-day on 0.5x MS medium containing 10 μM different ethylene antagoinsts were used as experimental set. Whole seedling was used for total RNA extraction and cDNA synthesis. cDNA labeling, array hybridization, and scanning followed by standard Affymetrix expression array protocol. Two independent sets of microarray analyses were performed in this assay.
2010-10-18 | E-GEOD-20897 | biostudies-arrayexpress
Project description:During tumor growth-when nutrient and anabolic demands are high-autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that Ras<sup>V12</sup> ; scrib<sup>-/-</sup> tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding, and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.
2021-09-24 | MTBLS2771 | MetaboLights
Project description:MDA-MB-231 EglN1-Flag IP-MS
| PRJEB101377 | ENA