GEO DataSets

(Submitter supplied) Soft rot or Rhizopus rot, caused by the fungal pathogen Rhizopus stolonifer, is an aggressive postharvest disease that affects many fruit and vegetables. We proposed that R. stolonifer displays a necrotrophic behavior when infecting fruit, actively killing the host tissues to complete its life cycle. We tested this hypothesis by identifying R. stolonifer infection strategies when interacting with four fruit hosts (tomato, grape, strawberry, and plum). more...

Organism:

Rhizopus stolonifer; Fragaria x ananassa; Prunus domestica; Solanum lycopersicum; Vitis vinifera

Type:

Expression profiling by high throughput sequencing

5 related Platforms

49 Samples

Download data: CSV

(Submitter supplied) To screen Botrytis genes activated in infection process, we performed gene expression profiling analysis using data obtained from RNA-seq of Botrytis cinerea cultured in vitro or infecting Arabidopsis leaves.

Organism:

Botrytis cinerea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32795

4 Samples

Download data: XLS

(Submitter supplied) The short-term, reversible process that allows plants to cope with immediate environmental fluctuations is often referred to as acclimation. Plant acclimation help maintain the balance of natural systems, supporting biodiversity and the services that ecosystems provide, such as carbon sequestration and water regulation. With climate change modifying the distribution area of plants and causing more frequent and severe weather events, knowledge of how plants acclimate can inform strategies to manage ecosystems and agriculture. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

54 Samples

Download data: TXT

(Submitter supplied) Nitrogen (N) can be absorbed by plants, thereby affects plant physiological activity, interferes gene expression, alters metabolite content and influences plant growth. However, the molecular mechanism underlying the potato tuberization response to nitrogen remains unclear. The plants were cultivated in the pots using N-deficient, N-Routine and N-sufficient conditions. Physiological response analysis, transcriptomics and metabolomics were performed on potato stolon exposed to Nitrogen stress. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27910

9 Samples

Download data: TXT

(Submitter supplied) Plants coexist in close proximity with numerous microorganisms in their rhizosphere. With certain microorganisms, plants establish mutualistic relationships that can confer physiological benefits to the interacting organisms, including enhanced nutrient assimilation or increased stress tolerance. The root-colonizing endophytic fungi Penicillium chrysogenum, Penicillium minioluteum, and Serendipita indica have been reported to enhance the drought stress tolerance of plants. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

24 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Talaromyces sp. F31

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34664

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. F51

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34663

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. F50

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34662

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. F2(2024)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34661

4 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by Mycobacterium tuberculosis has remained a leading cause of death worldwide even after decades of it being declared as global health emergency by the WHO. Newer drugs with novel modes of action are urgently needed to combat the threats imposed by the constantly emerging drug resistant strains. Natural products (NPs) derived anti-mycobacterials appear lucrative because of their complex structural features and unique cellular targets they bind to. more...

Organism:

Penicillium sp. C7(2024)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34660

4 Samples

Download data: TXT

(Submitter supplied) Soil water deficit (WD) is one of the most important abiotic stresses affecting plant survival and crop yield. Despite its economic relevance, many gaps remain in our understanding of how crops respond to WD, especially concerning the synergistic coordination of molecular and ecophysiological adaptations delaying plant mortality. In this study, we investigated the gene expression imposed by a progressive WD and combined it with measurements pointing to key ecophysiological thresholds in leaves of tomato plants. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28981

27 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL27957

20 Samples

Download data

(Submitter supplied) Background: Plant-unique RNA polymerase IV (Pol IV) governs the establishment of small RNA-directed DNA methylation (RdDM) and contributes to the maintenance of transposable element (TE) silencing. Pol IV-dependent RdDM is highly active during embryonic development, and its absence occasionally reduces seed sets in species with high TE content. However, the mechanism underlying embryonic development failure due to the loss of Pol IV-RdDM remains largely unclear. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL27957

6 Samples

Download data: TXT

(Submitter supplied) Background: Plant-unique RNA polymerase IV (Pol IV) governs the establishment of small RNA-directed DNA methylation (RdDM) and contributes to the maintenance of transposable element (TE) silencing. Pol IV-dependent RdDM is highly active during embryonic development, and its absence occasionally reduces seed sets in species with high TE content. However, the mechanism underlying embryonic development failure due to the loss of Pol IV-RdDM remains largely unclear. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

8 Samples

Download data: TXT

(Submitter supplied) Background: Plant-unique RNA polymerase IV (Pol IV) governs the establishment of small RNA-directed DNA methylation (RdDM) and contributes to the maintenance of transposable element (TE) silencing. Pol IV-dependent RdDM is highly active during embryonic development, and its absence occasionally reduces seed sets in species with high TE content. However, the mechanism underlying embryonic development failure due to the loss of Pol IV-RdDM remains largely unclear. more...

Organism:

Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27957

6 Samples

Download data: TXT

(Submitter supplied) Morchella sextelata, recognized for its medicinal properties and distinctive taste, is a highly valued edible mushroom. Despite its commercial importance, the mushroom's susceptibility to environmental factors and its reactions to herbicides commonly used in cultivation have not been extensively studied. This research aimed to explore how four prevalent herbicides—Trifluralin, Pendimethalin, S-metolachlor, and Acetochlor—affect the mycelial growth of Morchella sextelata. more...

Organism:

Morchella sextelata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34926

15 Samples

Download data: TXT

(Submitter supplied) By using RNA-seq analysis on purified extracellular vesicles from the infected tissue, we found that host plant Arabidopsis thaliana secretes a panel of messenger RNAs (mRNAs) in extracellular vesicles. These mobile plant mRNAs were delivered into cells of the interacting fungal pathogen Botrytis cinerea. While using Translating Ribosome Affinity Purification (TRAP) profiling and polysome analysis, we observed that the delivered host mRNAs were associated with active fungal polysomes isolated from the infected tissue, suggesting that they are translated in the fungal cells.

Organism:

Arabidopsis thaliana; Botrytis cinerea

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL31958 GPL31959 GPL26208

15 Samples

Download data: TXT

(Submitter supplied) The environmental conditions greatly influence tomato fruit quality, by affecting the expression of genes, the abundance of metabolites and the perception of sensorial attributes.In this study, a fruit transcriptome investigation, together with a sensory test and a metabolomic analysis were per-formed to evaluate the impact of the environment on two popular tomato cultivars grown in two Italian regions. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21167

12 Samples

Download data: TXT

(Submitter supplied) Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

Organism:

Oryza sativa; Arabidopsis thaliana; Solanum lycopersicum; Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

54 Samples

Download data: TXT

(Submitter supplied) Tomato (Solanum lycopersicum) is a major crop of high economic value. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild tomato species, has been used as breeding material for S. lycopersicum. In the present study a commercial tomato hybrid and two Introgression Lines (ILs), (S. more...

Organism:

Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27957 GPL33844

18 Samples

Download data: RESULTS