Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unravelling plant-density genetic architecture in canola

ABSTRACT: The intent of the experiment was to provide, from gene expression analysis, explanatory candidate genes related to density responses in Brassica napus (canola). We performed Illumina non-stranded single-end RNA-seq of leaves tissues in greenhouse-grown Lynx and Monty cultivars. We used a green filter that simulates neighboring plants along with control plants with no screen.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Brassica napus

SUBMITTER: Diego Sanchez

PROVIDER: E-MTAB-9342 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomics of shade avoidance and drought in Solanum tuberosum.

Project description:The intent was to study, from transcriptome analysis, shade and drought responses in Solanum tuberosum (potato). We performed Illumina 50 bp single-end RNA-seq in tissues of control and treated var. Spunta wild-type plants. Drought experiments also included two independent AtBBX21-overexpressing (BBX21-OE) potato lines.

2023-07-12 | E-MTAB-12771 | biostudies-arrayexpress

Physiological response and proteomics analysis of Castanopsis fissa under drought stress

Project description:Castanopsis fissa is an evergreen broad-leaved species of the cone genus Castanopsis in the family Fagaceae, which is widely distributed and is an excellent native species in Guangdong Province of China. This species has a well-developed root system, excellent soil-fixing power, and better soil and water conservation ability and has the characteristics of barren tolerance, strong sprouting power, abundant and easily decomposed dead leaves, etc. Therefore, C. fissa is not only a pioneer species for postdestruction sprouting forests but also a highly potential ecological public welfare forest tree species. Moreover, due to its beautiful shape, wide canopy and various colors, it has become an ideal tree for landscaping and ornamental purposes. However, there is a basic gap in knowledge in the reports on the drought resistance or drought tolerance genes of C. fissa. Based on the above details, in this study, 2-year-old C. fissa seedlings were used as the study material to investigate the physiological response under drought stress by a potted drought experiment, and we also compared and analyzed the differentially expressed proteins (DEPs) under different periods of drought stress by TMT quantitative labeling protein to prepare a preliminary study on the physiological response and proteomic mechanism of C. fissa adaptation to drought stress.

2023-07-24 | PXD038837 | Pride

Proteomics of non-host response in barley

Project description:Nonhost resistance, a resistance of plant species against all nonadapted pathogens, is considered the most durable and efficient immune system in plants. To increase our understanding of the response of barley (Hordeum vulgare L.) plants to infection by powdery mildew, Blumeria graminis f. sp. Tritici, we used quantitative proteomic analysis (LC-MS/MS). We compared the response of two genotypes of barley cultivar Golden Promise, wild type (WT) and plants with overexpression of phytoglobin (previously hemoglobin) class 1 (HO), which has previously been shown to significantly weaken non-host resistance. A total of 8804 proteins were identified and quantified, out of which the abundance of 1044 proteins changed significantly in at least one of the four comparisons (‘i’ stands for ‘inoculated’)- HO/WT and HOi/WTi (giving genotype differences), and WTi/WT and HOi/HO (giving treatment differences). Among these differentially abundant proteins (DAP) were proteins related to structural organization, disease/defense, metabolism, transporters, signal transduction and protein synthesis. More proteins changed in abundance in WT than in HO after inoculation and most DAP increased in abundance.

2020-08-18 | PXD015089 | Pride

iTRAQ-based quantitative proteomic analysis reveals new metabolic pathways responding to cold stress in two Winter Turnip Rape (Brassica rapa L.), part 2

Project description:Winter turnip rape (Brassica rapa L.) is a valuable ecologically beneficial oil crop that is produced mainly for its ability of conserving soil and water in winter and spring and its high quality edible oil in northwestern China. However, coldness and extremely low temperature negatively affects the growth and development of winter turnip rape, resulting in failure to overwinter and production in northwestern China. ‘Longyou 7’(Brassica rapa L.) and ‘Tianyou 4’ (Brassica rapa L.) are closely related plant species, but their cold tolerances are different. ‘Longyou 7’ is a cold-tolerant cultivar, ‘Tianyou 4’is a cold-sensitive cultivar. In this study, we used iTRAQ-based proteomics to compare quantitative changes in the proteome of two winter turnip rape leaves and roots in response to cold stress to elucidate the possible molecular mechanism underlying the ability of ‘Longyou 7’ to adapt to cold stress.

2019-11-12 | PXD008195 | Pride

iTRAQ-based quantitative proteomic analysis reveals new metabolic pathways responding to cold stress in two Winter Turnip Rape (Brassica rapa L.), part 1

2019-11-12 | PXD008194 | Pride

Cirsium.arvense.NewPhytol2013

Project description:transcription profiling of native and introduced populations of Cirsium arvense across three treatments to identify candidate genes involved in invasion

2013-05-05 | E-MTAB-1517 | biostudies-arrayexpress

Proteomic dataset for clematis in respose to heat stress

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

2020-06-04 | PXD018192 | Pride

New Insights into Heat Responses in Grape Leaves through Combined Phosphoproteomic and Acetylproteomic Analyses

Project description:Heat stress is a serious and widespread threat to the quality and yield of many crops, including grape (Vitis vinifera), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves from grape cultivated in four distinct temperature regimes. The phosphorylation or acetylation of a total of 1,011 phosphoproteins with 1,828 phosphosites, and 96 acetylproteins with 148 acetylsites, changed when plants were grown at 35°C, 40°C and 45°C in comparison with the proteome profiles of plants grown at 25°C. The greatest number of changes were observed at higher temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the responses to high temperatures. This is congruent with previous observations that alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat shock proteins were more associated with modifications in phosphorylation than in acetylation. Nineteen proteins were identified with changes in both phosphorylation and acetylation, consistent with crosstalk between these post-translational modifications.

2019-11-13 | PXD014090 | Pride

Proteome analysis reveals alterations in protein profile upon ectomycorrhiza establishment in oak roots

Project description:Trees establish a symbiotic relationship with specialized soil fungi, called ectomycorrhizae, which is essential for nutrition, growth and health of temperate forest ecosystems. Understanding the mechanisms governing the establishment and functioning of ectomycorrhiza is important because of the role of forests in sequestering CO2 and also to develop ways to optimize tree productivity and sustainability. Here, we investigated the response of an oak species to ectomycorrhiza formation using a two dimensional differential in gel electrophoresis (2D-DIGE) and MALDI-TOF/TOF mass spectrometry proteomics approach. At the root level, changes in the abundance of 34 unique oak proteins were detected and revealed proteins involved in carbon and energy metabolism, protein processing and degradation, response to oxidative stress, lipid metabolism/transport, nitrogen and phosphorous assimilation and cell wall modification. Proteins supporting the importance of the secretory pathway functioning, in particular of the endoplasmic reticulum, during ectomycorrhiza functioning were identified. These proteins were identified as components of the endoplasmic reticulum folding/chaperoning machinery and proteins involved in the ER quality control system. This study constitutes an important contribution for the understanding of the mechanisms underlying the response of plants to ectomycorrhizal symbiosis establishment.

2017-07-14 | PXD003009 | Pride

Comparative Proteome Profiling of Susceptible anComparative Proteome Profiling of Susceptible and Resistant Rice Cultivars Identified an Arginase Involved in Rice Defense Against Xanthomonas oryzae pv. oryzae d Resistant Rice Cultivars Identified an Arginase Involved in Rice Defense Against Xanthomonas oryzae pv. oryzae

Project description:Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight disease, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 protein groups. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase-1 in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type (WT). In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to WT. Mitochondrial localization of the selected arginase was further confirmed by fluorescent microscopy using GFP-tagged arginase. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of arginase in plant defense against Xoo.

2022-01-06 | PXD027569 | 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