Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Modeling protein destiny in developing tomato fruit

ABSTRACT: Proteomics and transcriptomics data of tomato fruits at 9 developmental stages were used to calculate with a mathematical model the rate constants of synthesis and degradation for over 1,000 proteins.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Solanum Lycopersicum

TISSUE(S): Pericarp

SUBMITTER: Mélisande Blein-Nicolas

LAB HEAD: Sophie Colombié

PROVIDER: PXD012877 | Pride | 2019-05-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20151106_bulk_01.raw	Raw
	20151106_bulk_01.xml	Xml
	20151106_bulk_02.raw	Raw
	20151106_bulk_02.xml	Xml
	20151106_bulk_03.raw	Raw

Items per page:

1 - 5 of 62

Publications

Modeling Protein Destiny in Developing Fruit.

Belouah Isma I Nazaret Christine C Pétriacq Pierre P Prigent Sylvain S Bénard Camille C Mengin Virginie V Blein-Nicolas Mélisande M Denton Alisandra K AK Balliau Thierry T Augé Ségolène S Bouchez Olivier O Mazat Jean-Pierre JP Stitt Mark M Usadel Björn B Zivy Michel M Beauvoit Bertrand B Gibon Yves Y Colombié Sophie S

Plant physiology 20190423 3

Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato (<i>Solanum lycopersicum</i>) fruit. Quantitative data were collected for transcripts and proteins during fruit development. Clustering analysis showed smaller changes in protein abundance compared to mRNA abundance. Furthermore, protein and transcrip ...[more]

PMID: 31015299

Publication: 1/2

Similar Datasets

Peptide Filtering and Quantification Methods

Project description:In bottom-up proteomics, data are acquired on peptides resulting from proteolysis. In XIC-based quantification, the quality of the protein abundance estimation depends on how peptide data are filtered and on which quantification method is used to sum up peptide intensities into protein abundances. So far, these two questions have been addressed independently. Here, we studied to which extent the relative performances of the quantification methods depend on the filters applied on peptide intensity data. To this end, we performed a spike-in experiment using Universal Protein Standard (UPS1) to evaluate the performances of five quantification methods, including TOP3, iBAQ, Average of all peptide intensities or log-intensities and intensity modeling, in five datasets obtained after application of four peptide filters based on peptide sharing between proteins, retention time variability, peptides occurrence and peptide intensity profiles. We showed that estimated protein abundances were not equally affected by filters depending on the computation mode (sum or average) and the type of data (intensity or log intensity) used in the quantification methods and that filters could have contrasting effects depending on the quantification objective (absolute or relative). Our results also indicate that intensity modeling was the most robust method, providing the best results in absence of any filter, but that the different quantification methods can reach similar performances when appropriate peptide filters are used. Altogether, our findings provide clues to best handle intensity data according to the quantification objective and to the experimental design.

2018-11-14 | PXD009740 | Pride

Genetic variation of maize responses to low temperatures in controlled conditions

Project description:Eighteen genetically-diverse maize hybrids (Zea mays, dent lines crossed to a flint inbred-line) were cultivated in a growth-chamber at optimal temperature (20°C) for three weeks. They were then submitted to three successive steps of decreasing temperature ( 16, 13 and 8.5°C). Each step lasted two days. Samples were taken on the youngest ligulated leaf (fourth or fifth leaf) at the end of the period at 20°C and at the end of each temperature step. Three replicates per genotype/ temperature combination were analyzed. Each replicate was made up of the mix of leaf samples from different plants.

2021-01-19 | PXD021790 | Pride

Cancer cell-derived ADAM15 dictates macrophage infiltration in colorectal tumors

Project description:Tumor progression and response to treatment is highly affected by interactions between cancer cells and the tumor microenvironment (TME). Many of the soluble factors and signaling receptors involved in this crosstalk are shed by a disintegrin and metalloproteinases (ADAMs). Upregulation of ADAM15 has been linked to worse survival in cancer patients and a tumor-promoting function both in vitro and in murine cancer models. Although ADAM15 has been involved in cell-cell and cell-extracellular matrix interactions, its role in the crosstalk between cancer cells and the TME in vivo remains unexplored. Therefore, we aimed to understand how ADAM15 regulates the cell composition of the TME and how it affects tumor progression. Here, we showed an upregulation of ADAM15 in tumor tissues from rectal cancer patients. Subcutaneous injection of wildtype and ADAM15-knockout CT26 colon cancer cells in syngeneic mice confirmed the pro-tumorigenic role of ADAM15. Profiling of tumors revealed higher immune cell infiltration and cancer cell apoptosis in the ADAM15-deficient tumors. Specifically, loss of ADAM15 led to a reduced number of granulocytes and higher infiltration of antigen-presenting cells, including dendritic cells and macrophages, as well as more T cells. Using in vitro assays, we confirmed the regulatory effect of ADAM15 on macrophage migration and identified ADAM15-derived CYR61 as a potential molecular mediator of this effect. Together, our data suggest that targeting ADAM15 could increase the infiltration of immune cells in colorectal tumors and thereby turn cold tumors hot, resulting in a potentially improved response to combined immunotherapy.

2023-07-24 | PXD041164 | Pride

Stroke Recovery Dominated by Dysregulation of Complement System – A Longitudinal Proteomics Pathway Analysis

Project description:Post-stroke recovery is an ongoing process as the brain attempts to reverse or minimize ischemia- induced disturbances in multiple biological systems. Currently, the longitudinal profile of molecular changes in patients post-stroke is relatively unknown. We therefore aimed to characterise biological pathways in plasma involved in post-stroke recovery using a discovery proteomics workflow coupled with a topological pathway systems biology approach. Blood samples (n = 180, EDTA plasma) were taken from a subgroup of 60 first episode stroke survivors from the Australian START cohort over 3 timepoints: 3-7 days (T1), 3-months (T2) and 12-months (T3) post primary event . Samples were analysed by liquid chromatography mass spectrometry (LC-MS) on the Q Exactive HF hybrid quadrupole-Orbitrap (Thermo-Fisher Scientific) using label-free quantification. The proteomics results were analysed for differential expression of all identified proteins for all available pairwise time-point comparisons. The resulting significant lists of proteins were then submitted for Gene Graph Enrichment Analysis (GGEA).

2020-08-31 | PXD015006 | Pride

Protein partners identification in Pyrococcus abyssi by nanoLC-MSMS

Project description:Recombinant aRNase J from P. abyssi, with C-terminal (His)6-tag (aRNase J-His), was produced, purified and used as baits for AP-MS experiments. In order to discriminate specific protein interaction from column background, we performed mock AP-MS analyses with P. abyssi cell extracts in absence of protein bait. In addition, to determine if some interactions are mediated through RNA or DNA, we implemented a nuclease treatment after incubating the cell extract with the bait. The co-purified partners were identified by bottom-up proteomic techniques coupled with mass spectrometry.

2020-01-21 | PXD015856 | Pride

Proteomic comparisons of autophagy mutant, salicylic acid defiscient mutant and wild type plants grown in ideal nutrition and in low nitrate and low sulfate conditions.

Project description:Genotypes used are Arabidopsis thaliana (L.) Col-0 wild-type, atg5.3 mutant (SALK_020601), sid2.2 (Dewdney et al., 2000) and the atg5.3/sid2.2 double mutant that has been previously characterized by Yoshimoto et al. Plant Cell (2009). Plants were cultivated under control conditions (ideal nutrition N+S+; 10mM NO3- and 0.266mM SO42-), low nitrate (N-; 2 mM NO3- and 0.266mM SO42-), or low sulfate (S-; 10mM NO3- and 0.016mM SO42-) conditions, under in short days (160 micromol.m-2.s-1; 8 h light, 16 h dark) in growth chamber as described by Havé et al. 2019 New Phytologist. Rosettes were harvested at vegetative stage 60 days after sowing, 2-3 hours after the beginning of the photoperiod. Two consecutive cultures (C1 and C2) were performed at several month interval. For each culture, three plant repeats (R1-R3) were collected, each repeat was a mix of >6 rosettes. Details can be found in Havé et al. (2019) New Phytologist (doi: 10.1111/nph.15913). Associated publications are Havé et al. (2018) JXB (doi:10.1093/jxb/erx482), Havé et al. (2019) New Phytologist (doi: 10.1111/nph.15913) and Luo et al 2020 JXB (doi:10.1093/jxb/eraa337)

2023-10-27 | PXD029638 | Pride

HP1 wa191.OR Head Nuclei

Project description:modENCODE_submission_957 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determe the locations of 125 chromosomal proteins and histone modifications across the Drosophila melanogaster genome. The proteins and modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: CHIP-chip EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Oregon-R; Developmental Stage: Mixed Adult; Genotype: wild type; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Developmental Stage Mixed Adult; organism part ; Antibody HP1 wa191 (target is HP1a); Strain Oregon-R

2010-08-10 | E-GEOD-23461 | biostudies-arrayexpress

Human pituitary adenoma MiRnome

Project description:Small RNA (<100 bases in length) were purified from total RNA using miRNeasy kit (Qiagen), then sequenced. Libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq small RNA protocol (Illumina), starting from 1 µg of high quality total RNA. Single read (1 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on miRBase v.2052, then counted with STAR (v.2.5.2a). Counts were normalized with DESeq v1.30.0

2020-05-01 | E-MTAB-7969 | biostudies-arrayexpress

NGF and proNGF activate functionally distinct mRNAs in PC12 cells: an early gene expression profiling

Project description:The biological activities of NGF and of its precursor proNGF are quite distinct, due to different receptor binding profiles, but nothing is known about how proNGF regulates gene expression. We performed experiments to address this question, by verifying whether a proNGF specific transcriptional signature, distinct from that of NGF, could be identified. To this aim, we studied gene expression regulation by proNGF and NGF in PC12 cells incubated for 1 and 4 hours with recombinant NGF and proNGF, in its wild-type or in a furin-cleavage resistant form. mRNA expression profiles were analyzed by whole genome microarrays at these early time points, in order to identify specific profiles of NGF and proNGF. Three-conditions experiment: PC12 cells were treated with NGF, wild type proNGF precursor (proNGF-WT), furin resistant mutated proNGF precursor (proNGF-KR) for 1 and 4 hours. Two biological replicates were performed for each condition. RNA was extracted after 1 hour and 4 hours of treatment for each treatment.

2012-01-09 | E-GEOD-26528 | biostudies-arrayexpress

Caco-2 cells: 21-days differentiated cells maintained with the low density protocol (LD cells) vs 21-days differentiated cells maintained with the high density protocol (HD cells)

Project description:Transcriptional profile of 21-days differentiated LD Caco-2 cells compared to 21-days differentiated HD Caco-2 cells. Goal was to find some differences in the genome profile of the LD and HD Caco-2 cells that could be addressed to the different protocols used for the line maintenance. Two-condition experiment: 21-days differentiated Caco-2 cells maintained with the LD protocol and 21-days differentiated Caco-2 cells maintained with the HD protocol. Dye-swap technical replicates.

2011-04-25 | E-GEOD-21518 | 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