Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic dataset for clematis in respose to heat stress

ABSTRACT: This project presents the raw data about pretomic of two clematis seedings in response to heat stress at 38 oC for 3 h

INSTRUMENT(S): Q Exactive

ORGANISM(S): Clematis Chinensis

TISSUE(S): Leaf

SUBMITTER: Mingnan Qu

LAB HEAD: Mingnan Qu

PROVIDER: PXD018192 | Pride | 2020-06-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Proteome and transcriptome reveal the involvement of heat shock proteins and antioxidant system in thermotolerance of Clematis florida.

Jiang Changhua C Bi Yuke Y Mo Jianbin J Zhang Ruyao R Qu Mingnan M Feng Shucheng S Essemine Jemaa J

Scientific reports 20200601 1

Clematis florida Thun (CfT) is an ornamental and medicinal plant. It is a cold resistant but heat sensitive species and deserves to be further investigated to improve its adaptability to heat stress. Exploring the molecular mechanism potential via an omic-analysis constitutes a promising approach towards improving heat tolerance of CfT. Two CfT lines, heat resistance (HR) and heat sensitive (HS), with differential thermotolerance capacities were used for the integrative analyses of proteomics an ...[more]

PMID: 32483281

Similar Datasets

Inferior Temporal Gyrus in Human Ageing: a Quantitative Protein Profiling Work based on Chinese Human Brain Bank

Project description:The temporal lobe is the cerebral cortex with critical function. The superior and middle gyrus of temporal lobe have been well studied, however, present perceptions on inferior temporal gyrus remains limited. The understanding of age-related protein profile change in human inferior temporal gyrus has not yet been well established. This 3-plex TMT labeled proteomic study is performed based on the human brain bank at the Chinese Academy of Medical Sciences & Peking Union Medical College. Age distribution of the donors ranges from 22 to 90 years old, and were assigned to three age groups: 20-50, 50-70, and 70-90 years of death age. In this ageing cohort, no neurodegenerative disorders or major stroke events were identified via standard neuropathological classification. Proteomics and bioinformatics strategies were applied to identify the perturbations of protein expression and associated pathways. Among all the ITG samples, 3113 proteins were isolated, with 37 proteins upregulated and 21 proteins downregulated.

2015-12-07 | PXD002528 | Pride

Structural Alternation in Heat Shock Proteins of Activated Macrophages

Project description:The inflammatory response of macrophages is an orderly and complex process under strict reg-ulation accompanied by drastic changes in morphology and functions. It is predicted that pro-teins will undergo structural changes during these finely regulated processes. However, changes in structural proteome in macrophages during the inflammatory response remain poorly char-acterized. In the present study, we applied limited proteolysis coupled mass spectrometry (LiP-MS) to identify proteome-wide structural changes in lipopolysaccharide (LPS)-activated macrophages. We identified 386 structure-specific proteolytic fingerprints from 230 proteins. Using GO molecular function enrichment, we discovered that proteins with altered structures were enriched into unfolded protein binding and protein folding chaperone, in which HSP60 was ranked as the most changed protein. We verified the structural changes in HSP60 by using cellular thermal shift assay (CETSA) and native CETSA. Our results showed that the thermal sta-bility of HSP60 was enhanced in activated macrophages and formed a HSP10-less complex. In conclusion, we demonstrate that in situ structural systems biology is an effective method to characterize proteomic structural changes and reveal that the structures of chaperone proteins vary significantly in macrophage activation.

2022-02-17 | PXD029672 | Pride

Protein Profile Changes in the Frontotemporal Lobes in Human Severe Traumatic Brain Injury

Project description:Severe traumatic brain injury (sTBI) is a serious public health issue with high morbidity and mortality rates. Previous proteomic studies on sTBI have mainly focused on human cerebrospinal fluid and serum, as well as on brain protein changes in murine models. However, human proteomic data in sTBI brain is still needed. We used proteomics and bioinformatics strategies to investigate variations in protein expression in human brains after sTBI, using samples from the Department of Neurosurgery, Affiliated Hospital of Hebei University (Hebei, P.R. China). Our proteomics data identified 4031 proteins, of which 162 proteins were overexpressed and 5 proteins were downregulated. The biological pathways that showed significant changes in protein expression according to bioinformatics analysis were glial cell differentiation, complement activation, apolipoprotein catalysis in statin pathway, and the blood coagulation cascade. Western blot verification of protein changes in a subset of the available tissue samples showed results that were consistent with the proteomics data. This study is one of the first to investigate the whole proteome of human sTBI brains, and provides a characteristic signature and overall landscape of the sTBI brain proteome.

2016-04-15 | PXD002783 | Pride

TMT analysis of tissue proteomics in bevacizumab-resistant xenograft tumor tissuein nude mice

Project description:TMT proteomics was used to detect the difference in protein expression of bevacizumab-resistant xenograft tumor tissue in nude mice.

2022-10-13 | PXD030202 | Pride

Presynaptic proteins in the orbitofrontal cortex predict Alcohol Use Disorder

Project description:Alcohol use disorder (AUD) is a life-threatening disease characterized by compulsive drinking, cognitive deficits, and social impairment that continue despite negative consequences, which are driven by dysfunction of cortical areas, such as the orbitofrontal cortex (OFC), that normally balances decisions related to reward and risk. In this study, proteomics and machine learning analysis of post-mortem OFC brain samples collected from individuals with AUD revealed dysregulation of presynaptic (e.g., AP2A1) and mitochondrial proteins that predicted the occurrence and severity of AUD. Alcohol-sensitive OFC proteins also mapped to abnormal social behaviors and interactions. Validation using reverse genetics, we found that prefrontal Ap2a1 regulates alcohol drinking in genetically diverse mouse strains. Furthermore, we demonstrated sexual dimorphism in human OFC proteins that regulate extracellular matrix structure and signaling. Together, these findings highlight the impact of excessive alcohol consumption on the human OFC proteome and identify important cross-species cortical mechanisms underlying AUD.

2023-10-09 | PXD041727 | Pride

Proteome of Agave angustifolia Haw.: insights about metabolism of amino acids in albino plantlets

Project description:Amino acids (AA) are essential molecules for life because they are precursors for the synthesis of proteins and other organic compounds. Their metabolism in plants involves more than one cellular compartment, among which the chloroplast plays a key role. From the 20 essential AA, ten (Arg, Lys, Thr, Leu, Ile, Val, Trp, Phe, Tyr and His) are only synthesized in the plastids and seven (Asp, Cys, Gln, Glu, Gly, Ser and Met) can be synthesized in both chloroplast and other parts of the cell. Despite knowing the roles of AA in plant physiology, little has been assessed in plants with albino phenotypes, lacking chloroplasts. To assess the effect of chloroplast biogenesis disturbances on AA metabolism in albino and variegated somaclonal variations of Agave angustifolia Haw., a comparative proteomic based TMT- synchronous precursor selection (SPS)-MS3 strategy was used to determine the status of AA biosynthetic pathways. Besides the 20 essential AA was quantified to underpin proteomics finding. A total of 2,442 different proteins were identified in the proteome of the somaclonal variants, from which 82 correspond to enzymes participating in AA biosynthesis. From these 82, 32 proteins were differentially accumulated. On the other hand, the concentration of 16 and 12 of the AA synthesized by the chloroplast were over-accumulated in the variegated and albino somaclonal variant, respectively. In plantlets devoid of functional chloroplasts, there is a surprising increase of AA and key enzymes of the AA biosyntethic pathways, compared to green plantlets. This could suggest que la activation of AA biosynthesis is key to sustaining albino and variegated plantlets survival that lack chloroplasts.

2024-01-29 | PXD039512 | Pride

Integrative analysis of transcriptomics and proteomics of Longissimus dorsi muscle to identify proteins underlying intramuscular fat content in pigs

Project description:The Laiwu pig is famous for its excessively higher level of IMF content, however, the exact regulatory mechanism is still unknown. The intramuscular fat content (IMF) is an economically important traits in pigs, which is controlled by multiple genes and biological pathways. In the present study, we performed an integrated transcriptome-assisted label-free quantitative proteomic analysis of longissimus dorsi (LD) muscle in Laiwu pigs at the fastest IMF deposition stage. A total of 5074 unique proteins were identified and 191 were differentially abundant proteins (DAPs) (> 1.2-fold cutoff, p < 0.05), which were hierarchically clustered in the LD muscle over two developmental stages from 120 d to 240 d. Proteins participating in the regulation of lipolysis in adipocytes and AMPK signaling pathway were identified. Six proteins were analyzed using parallel reaction monitoring (PRM) to confirm the reliability of the TMT proteomic analysis. Association networks of differentially abundant proteins revealed that these DAPs were mainly involved in ribosome biosynthesis in eukaryotic species. A comparasion between transcriptomic (mRNA) and proteomic data revealed seven differentially expressed genes corresponding to DAPs. This study, for the first time, provides some data for the elucidation of the molecular mechanism of IMF deposition in pigs.

2020-01-09 | PXD011718 | Pride

Human menstrual blood-derived stem cell transplantation suppresses liver injury in DDC-induced chronic cholestasis

Project description:Increasing studies suggested the treatment potential of mesenchymal stem cells in variety diseases. Evidence showed that MSCs could promote injured tissue repair and improve disease mortality. These indicated that MSC transplantation may be an ideal candidate for cholestasis treatment.We found that MenSC transplantation could significantly improve the symptoms and pathological changes of DDC-induced cholestasis liver injury in mice.

2022-02-16 | PXD028425 | Pride

HDX-MS data of trigger factor and GAPDH binding

Project description:We present HDX-MS data of the trigger factor:GAPDH complex to define the interaction sites for GAPDH on trigger factor and the structure of GAPDH in the bound state.

2022-06-07 | PXD029364 | Pride

A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts

Project description:Chemical activators and inhibitors are useful probes to identify substrates and downstream effects ofenzymes; however, due to the complex signaling environment within cells, it is challenging to distinguishbetween direct and indirect effects. This is particularly the case for phosphorylation, where a single(de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additionalcomplication arises when a single catalytic entity, which acts in form of many different holoenzymes withdifferent substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turnwhich of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to studytargets of drugs do not address these challenges. Here, we tackle this by studying the modulation of proteinphosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, byusing a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDPwith in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and beginto separate direct and indirect effects. Together with experiments analyzing which holoenzymes areparticularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complexnetwork of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemicalmodulators with complex mode of action in general.

2024-01-12 | PXD044415 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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