Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An engineered promoter-reporter for insoluble protein in Saccharomyces cerevisiae

ABSTRACT: Saccharomyces cerevisiae proteome response upon expression of 3 proteins (mKate2, mKate2-MBP and mKate2-LipPks1) was studied by shotgun proteomics.

INSTRUMENT(S): Q Exactive HF-X, Q Exactive HF

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: David Romero-Suarez

LAB HEAD: Michael Krogh Jensen

PROVIDER: PXD021470 | Pride | 2021-02-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PD_Contaminants_2015_5.fasta	Fasta
	Prot36.mgf	Mgf
	Prot36.msf	Msf
	Prot36.mzIdentML	Mzid
	Prot36.pep.xml	Pepxml

Items per page:

1 - 5 of 21

Publications

A Reporter System for Cytosolic Protein Aggregates in Yeast.

Romero-Suarez David D Wulff Tune T Rong Yixin Y Jakočiu Nas Tadas T Yuzawa Satoshi S Keasling Jay D JD Jensen Michael K MK

ACS synthetic biology 20210212 3

Protein misfolding and aggregation are linked to neurodegenerative diseases of mammals and suboptimal protein expression within biotechnology. Tools for monitoring protein aggregates are therefore useful for studying disease-related aggregation and for improving soluble protein expression in heterologous hosts for biotechnology purposes. In this work, we developed a promoter-reporter system for aggregated protein on the basis of the yeast native response to misfolded protein. To this end, we fir ...[more]

PMID: 33577304

Similar Datasets

Identification of microRNAs involved in acute rejection and spontaneous tolerance in murine hepatic allografts

Project description:Graft acceptance without the need for immunosuppressive drugs is the ultimate goal of transplantation therapy. In murine liver transplantation, allografts are accepted across major histocompatibility antigen complex barriers without the use of immunosuppressive drugs and constitute a suitable model for research on immunological rejection and tolerance. MicroRNA (miRNA) has been known to be involved in the immunological responses. In order to identify mRNAs in spontaneous liver allograft tolerance, miRNA expression in hepatic allografts was examined using this transplantation model. According to the graft pathological score and function, miR-146a, 15b, 223, 23a, 27a, 34a and 451 were upregulated compared with the expression observed in the syngeneic grafts. In contrast, miR-101a, 101b and 148a were downregulated. Our results demonstrated the alteration of miRNAs in the allografts and may indicate the role of miRNAs in the induction of tolerance after transplantation. Furthermore, our data suggest that monitoring the graft expression of novel miRNAs may allow clinicians to differentiate between rejection and tolerance. A better understanding of the tolerance inducing mechanism observed in murine hepatic allografts may provide a therapeutic strategy for attenuating allograft rejection. B10.BR mice were used as donors and B10.D2 mice were used as recipients. Liver allo-transplantation surgery on the mice was performed in this combination. Three mice from each group were sacrificed, and the liver grafts were removed on days 5, 8, 14 and 100 after transplantation. Total RNA, including miRNA was isolated. 100ng of total RNA was labeled by Cy3 and used as probe for hybridization to the microarray.

2014-10-21 | E-GEOD-52164 | biostudies-arrayexpress

Rational Design of Small Molecules as Vaccine Adjuvants

Project description:Analysis of whole mouse muscle and inguinal lymph node gene expression signature induced after 24h by in-vivo intramuscularly administration of R848, SMIP-7.7, SMIP-7.8 and 4%DMSO controls. Analysis of whole mouse muscle and inguinal lymph node gene expression signature induced after 6h by in-vivo intramuscularly administration of R848 and SMIP-7.2 in 1% DMSO, and SMIP-7.10 and SMIP-7.10+alum in Buffer.

2015-11-02 | E-MTAB-2948 | biostudies-arrayexpress

Pinctada fucata martensii mantle edge tissue LC-MS/MS

Project description:We have got a yellow shell variety of Pinctada fucata martensii after years of artificial breeding. To identify differentially expressed genes between yellow shell and normal black shell pearl oysters, we performed label-free proteomic analyses by LC-MS using mantle edge tissues.

2019-11-13 | PXD012211 | Pride

Proteomic raw data for Mettl3 Ctrl and RKO mice

Project description:The purpose of this project is to explore the changes in signaling pathways after Mettl3 knockout, and to identify potential downstream target proteins of Mettl3 along with the signaling pathways they are involved in. Ultimately elucidating the molecular mechanisms underlying Mettl3 pathogenesis. Retina of control and Mettl3 knockout mice were collected, and samples were then used for proteomic analysis. After tissue collection, a series of cutting-edge technologies, including protein extraction, enzyme digestion, liquid chromatography-tandem mass spectrometry, and bioinformatics analysis, were employed to investigate the quantitative proteome of the samples.

2024-10-12 | PXD056750 | Pride

Proteomic raw data for ctrl HRECs, CAPSL knockdown HRECs, and CAPSL overexpression HRECs

Project description:The purpose of this project is to explore the changes in signaling pathways after CAPSL knockdown and overexpression, and to identify potential downstream target genes of CAPSL along with the signaling pathways they are involved in. Ultimately elucidating the molecular mechanisms underlying CAPSL pathogenesis. HRECs were transfected with ctrl shRNA, CAPSL knockdown shRNA and LentiOE CAPSL. The cells were then collected at least 72h after transfection, and samples were then usd for proteomic analysis. After cell collection, a series of cutting-edge technologies, including protein extraction, enzyme digestion, liquid chromatography-tandem mass spectrometry, and bioinformatics analysis, were employed to investigate the quantitative proteome of the samples.

2024-09-04 | PXD051696 | Pride

Quantitative proteomic analysis of pseudomonas aeruginosa samples

Project description:Ionizing irradiation kills pathogens by destroying nucleic acids while retaining the immunogenicity of pathogen proteins. However, the overall proteome of bacteria exposed to X-ray irradiation still remain unclear. This experiment was aimed to investigate the proteome changes of the laboratory Pseudomonas aeruginosa PAO1 strain after exposure to X-ray irradiation. A total of 2963 proteins were identified in this study, of which 2599 proteins contained quantitative information. If the differential expression change threshold is 2 times, and the statistical test t-test p-value <0.05 is the significance threshold, then among the quantified proteins, the expression of 48 proteins was up-regulated and 8 protein expression was down-regulated. Based on the above data, we performed a systematic bioinformatics analysis of all identified proteins, and performed functional classification, functional enrichment, and clustering analysis based on functional enrichment for all differentially expressed proteins. Combined with the above information, it provides a reference direction for further investigation in the biological effect on P. aeruginosa PAO1 and its MV formation under X-ray irradiation.

2020-12-14 | PXD019035 | Pride

Combined transcriptome and proteome profiling for role of pfEMP1 in antimalarial mechanism of action of dihydroartemisin

Project description:Malaria parasites induce morphological and biochemical changes in the membranes of parasite-infected red blood cells (iRBCs) for propagation. Artemisinin combination therapies are the first-line antiplasmodials in endemic countries. However, the mechanism of action of artemisinin is unclear, and drug resistance decreases long-term efficacy. To understand whether artemisinin targets or interacts with iRBC membrane proteins, this study investigated the molecular changes caused by dihydroartemisin (DHA), an artemisinin derivative, in Plasmodium falciparum 3D7 using a combined transcriptomic and membrane proteomic profiling approach.

2022-02-15 | PXD028062 | Pride

Expression data from Panc1 pancreatic epithelial cells

Project description:KrÃ¼ppel-like factors (KLFs) are a group of master regulators of gene expression conserved from flies to human. However, scant information is available on either the mechanisms or functional impact of the coupling of KLF proteins to chromatin remodeling machines, a deterministic step in transcriptional regulation. In the current study, we use genome-wide analyses of chromatin immunoprecipitation (ChIP-on-Chip) and Affymetrix-based expression profiling to gain insight into how the KLF11, a human transcription factor involved in tumor suppression and metabolic diseases, works by coupling to three co-factor groups: the Sin3-histone deacetylase system, WD40-domain containing proteins, and the HP1-histone methyltransferase system. We utilized genome-wide expression analysis of wild type KLF11 and three mutants that disrupt KLF11-chromatin machinery interactions to examine the relationship of the transcription factor and chromatin systems in the regulation of gene networks. Panc1 epithelial cells were plated at a density of 1x10^6 cells/100mm dish and transduced with empty vector, KLF11, KLF11-A347S, KLF11-486, or KLF11-EAPP adenovirus at an MOI of 150. RNA was prepared as previously described from pooled biological triplicates.

2014-08-01 | E-GEOD-56778 | biostudies-arrayexpress

B. subtilis response to rotten meat volatiles.

Project description:To find a promoter upregulated in the presence of rotten meat, we exposed B. subtilis 168 to the volatiles of rotten meat (mixed beef/pork) and performed a microarray comparing it to B. subtilis which was not exposed to the meat. The results where used to build iGEM Groningen 2012s Food Warden, a spoiled meat detector. Find more information at: 2012.igem.org/Team:Groningen One condition design; including dye swap, two technical replicates and two experimental replicates

2013-09-04 | E-GEOD-50538 | biostudies-arrayexpress

Proteomic Profiling Identifies Novel Diagnostic Biomarkers and Molecular subtypes for Mucinous Tubular and Spindle Cell Carcinoma of the Kidney

Project description:Mucinous tubular and spindle cell carcinoma (MTSCC) is a relatively rare renal epithelial neoplasm resembling type 1 papillary renal cell carcinoma (PRCC) morphologically and immunohistochemically. The accurate diagnosis of MTSCC remains a challenge. Here, by using proteomic profiling, we characterized MTSCC and PRCC to identify diagnostic biomarkers. We found that MTSCC tumor proteome was significantly enriched in B cell-mediated immunity when compared with the proteome of adjacent normal tissues of MTSCC or tumors of PRCC. Importantly, we identified MZB1, VCAN, and SOSTDC1 as diagnostic biomarkers to distinguish MTSCC from PRCC, with an AUC of 0.9839 when combined. MZB1 was inversely correlated with tumor clinical stage and may play an anti-tumor role by activating the complement system. Finally, unsupervised clustering revealed two molecular subtypes of MTSCC, displaying different morphology, expression signatures of oxidative phosphorylation, and aggravation. In summary, our analyses identified a three-protein diagnostic panel and molecular subtypes for MTSCC.

2022-02-11 | PXD027972 | Pride

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