Transcription profiling of tomato strains during fruit set
Ontology highlight
ABSTRACT:
ORGANISM(S): Lycopersicon esculentum
SUBMITTER: Pierre Frasse
PROVIDER: E-MEXP-1617 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:identify the key genes and construct the gene regulatory networks involved in the flowering process of "sijimi" longan
2017-07-24 | PXD006710 | Pride
Project description:Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in Arabidopsis and especially other plant species engaged with global proteome assays. Here, we present large-scale protein profiling of tomato fruit across two key tissues and five developmental stages. This was accomplished by means of a shotgun proteomic assay comprising prior multi-step peptide fractionation followed by nano flow liquid chromatography coupled with high-resolution mass-spectrometry. A total of 7738 individual proteins were identified and reliably measured at least in one of the analysed tissues or stages. The detection of 115 putative transcription factors (TFs) further demonstrated the depth of our assay since a small number of TF proteins are typically detected in plant proteomics assays. Among this TFs set, 61 were differentially expressed in fruit development including renowned ripening regulators and elements of ethylene signalling. Curiously, we measured more than 80% of the predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were detected including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns which is most significant in light of the weak transcript-protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique, protein level view of skin and flesh tissues in developing fruit. This study adds a different perspective to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post-translational research in tomato and additional species which is presently focused on transcription.
2017-01-30 | PXD004887 | Pride
Project description:We introduced the GAME1i construct into the indeterminate M82 cultivar by crossing, obtaining plants that displayed a phenotype of severe growth retardation, deformed leaves and abortion of flower buds . In addition, leaves of these plants exhibited dark necrotic spots resembling symptoms typically seen after infection of tomato by pathogenic bacteria like Xanthamonas campestris pv. vesicatoria (Xcv) or Pseudomonas syringae pv. tomato (Pst) . As no other tomato lines grown in the same greenhouse at the same time showed similar disease-like symptoms, we hypothesized that silencing GAME1 might mimic induction of disease symptoms in the absence of a pathogen. Indeed, we were able to isolate neither Xcv nor Pst (or other putative pathogens) from GAME1i leaves that displayed necrotic spots. Microarray analysis was performed to examine if the transgene, and possibly, the corresponding changes in the metabolic profile, induced the plant response system at the transcriptional level.
2011-11-28 | E-MEXP-3455 | biostudies-arrayexpress
Project description:We measured transcriptional profiles of individuals of Andropogon gerardii and Sorghastrum nutans, two C4 grass species native to North American grasslands, in a field experiment in which both temperature and precipitation have been manipulated to simulate key aspects of forecasted climate change. 99 samples were analyzed.
2012-05-11 | E-GEOD-35492 | biostudies-arrayexpress
Project description:This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage. Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. Five adjacent stages have disproportionately more significant changes in gene expression (>200 genes) relative to other stages: four to eight and eight to sixteen cell stages, onset of circulation, pre- and post-hatch, and during complete yolk absorption. The fewest differences among adjacent stages occur during gastrulation. Yet, at stage 16 (pre-mid-gastrulation), the largest number of genes has peak expression. This stage has an over-representation of genes in oxidative respiration and protein expression (ribosomes, translational genes and proteases). Unexpectedly, among all ribosomal genes, both strong positive and negative correlations occur. Similar correlated patterns of expression occur among all significant genes. These data provide statistical support for the temporal dynamics of developmental gene expression during all stages of vertebrate development. A double-loop design was used for the microarray hybridizations, where each sample is hybridized to 2 arrays using both Cy3- and Cy5-labelled fluorophores (Kerr and Churchill 2001a; Kerr and Churchill 2001b). The loop consisted of Cy3- and Cy5-labelled embryo aRNAs from 4 biological pools for each of 40 stages (S). In total, 160 biological pools were hybridized to 80 microarrays. Each array had different combinations of biological pools (Altman and Hua 2006). The double loop formed was S1M-bM-^FM-^R S2 M-bM-^FM-^R S3M-bM-^FM-^R M-bM-^@M-& S40M-bM-^FM-^R S1 and S40M-bM-^FM-^R S39M-bM-^FM-^R S38M-bM-^FM-^R M-bM-^@M-& S2M-bM-^FM-^R S1 M-bM-^FM-^R S40, where each arrow represents a separate hybridization (array) with the biological pool at the base of the arrow labeled with Cy3 and the biological pool at the head of the arrow labelled with Cy5.
2011-04-19 | E-GEOD-21372 | biostudies-arrayexpress
Project description:This study explores the synergistic effects of two model PAHs, an aryl hydrocarbon receptor (AHR) agonist (M-NM-2-naphthoflavone) and a cytochrome P4501A (CYP1A) inhibitor (M-NM-1-naphthoflavone), on gene expression in stage 31 embryos from two different population. One population (Elizabeth River population) is relatively resistant to the pollutants in its environment. A loop design (Figure 5) was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores (Kerr and Churchill, 2001). The loop consisted of Cy3 and Cy5 labeled embryo aRNAs from 4 biological samples and six different treatments (T1-T6: control, 1 M-NM-<g/L BNF, 50 M-NM-<g/L ANF, 100 M-NM-<g/L ANF, 1 M-NM-<g/L BNF + 50 M-NM-<g/L ANF, 1 M-NM-<g/L BNF + 100 M-NM-<g/L ANF). In total, 48 biological samples were hybridized to 24 microarrays. Each array had different combinations of biological samples, so that the most direct comparisons (i.e., 50 M-BM-5g/L ANF resistant embryo and 50 M-BM-5g/L sensitive embryo) are hybridized to the same array. The loop formed was T1SM-bM-^FM-^R T1R M-bM-^FM-^R T2SM-bM-^FM-^R T2R M-bM-^FM-^RT3SM-bM-^FM-^R T3RM-bM-^FM-^R T4SM-bM-^FM-^R T4RM-bM-^FM-^R T5SM-bM-^FM-^R T5R M-bM-^FM-^R T6SM-bM-^FM-^RT6RM-bM-^FM-^R T1SM-bM-^FM-^R T2S M-bM-^FM-^R T3S M-bM-^FM-^R T4S M-bM-^FM-^R T5S M-bM-^FM-^R T6S M-bM-^FM-^R T1S M-bM-^FM-^R T1R M-bM-^FM-^R T2R M-bM-^FM-^R T3R M-bM-^FM-^R T4R M-bM-^FM-^R T5R M-bM-^FM-^R T6R, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological pool at the head of the arrow labeled with Cy5. T1-6 is treatment, and S and R represent sensitive and resistant embryos.
2013-09-30 | E-GEOD-47654 | biostudies-arrayexpress
Project description:Artemisia annua is well known for biosynthesizing artemisinin, which is the primary therapeutic approach against malaria. It was reported that treatment with leaf of A. annua showed better effect and less tendency of developing drug resistance than purified artemisinin, suggesting other components in A. annua may contribute to the therapeutic efficacy. Here, we conducted a global proteomic profiling of A. annua with identification of a total of 13,403 proteins based on the genome sequence annotation database. Furthermore, we generated a spectral library to perform quantitative proteomic analysis using data independent acquisition mass spectrometry (DIA-MS). Specifically, we comprehensively quantified and compared proteins between two chemotypes that produce high (HAP) and low (LAP) artemisinin content, respectively. 182 proteins were identified with abundance significantly different between these two chemotypes. Overall, our current study globally identified the proteome of A. annua and quantitatively compared the targeted sub-proteomes between the two cultivars of HAP and LAP, providing systematic information on metabolic pathways of A. annua and facilitating identification of good chemotypes for producing anti-malaria compounds.
2020-04-27 | PXD015547 | Pride
Project description:The protein content determines the cell state. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown. We quantified 47,535 mRNAs and 3,742 proteins in filling grain of wheat under two thermal environments. The impact of mRNA abundance and sequence features which implicated in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency mainly drive the changes in protein expression under heat stress, and their combined contribution explains 58.2% and 66.4% of protein variation in 30 and 40 °C, respectively. Of which, transcription contributes more to the alteration in protein content under 40 °C (31%) than to 30 °C (6%). Codon usage plays a stable and powerful role in protein expression under heat stress, even surpassing transcription. What’s more, the usage of AAG is a key factor regulating rapid protein expression under heat stress.
2021-03-24 | PXD021460 | Pride
Project description:This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl). The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA). For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle. At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation. A loop design was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores. We used three loops in which each loop consisted of Cy3- and Cy5-labeled embryo aRNAs from 12 samples: one sample from each population-treatment-time combination. Within a population-treatment-time, embryos were randomly assigned to one of the three loops. In total, 36 embryos were hybridized to 36 microarrays. The loops formed were SC5C→ SC5P → NBH5C→ NBH5P →SC10C→ SC10P→ NBH10C→ NBH10P → SC15C→ SC15P → NBH15C → NBH15P → SC5C, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological sample at the head of the arrow labeled with Cy5. SC represents the Scorton Creek, Sandwich, MA population (reference), NBH represents the New Bedford Harbor, MA population, C represents control dose (DMSO), P represents the PCB-126 dose, 5 represents 5 dpf, 10 represents 10 dpf and 15 represents 15 dpf.
2011-06-06 | E-GEOD-25245 | biostudies-arrayexpress
Project description:We have used a microarray approach to study the effects of the Potato Virus X Potexvirus (PVX)-specific P25 VRS protein on the transcript profile of tobacco plants, when expressed as a transgene in these plants.
2013-02-14 | E-MEXP-3750 | biostudies-arrayexpress