GEO DataSets

(Submitter supplied) Tomato is a major global crop however its production is limited by Botrytis cinerea. Due to the toxicity of post-harvest pesticide application, alternative control methods such as priming are being investigated. Plants were treated with β-aminobutyric (BABA) at two developmental stages and resistance against B. cinerea was tested in fruit tissue and in progenies. DNA methylation and RNA sequencing were conducted to characterise the (epi)genetic changes associated with long-lasting resistance. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

29 Samples

Download data: TXT

(Submitter supplied) Tomato is a major global crop however its production is limited by Botrytis cinerea. Due to the toxicity of post-harvest pesticide application, alternative control methods such as priming are being investigated. Plants were treated with β-aminobutyric (BABA) at two developmental stages and resistance against B. cinerea was tested in fruit tissue and in progenies. DNA methylation and RNA sequencing were conducted to characterise the (epi)genetic changes associated with long-lasting resistance. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL27957

12 Samples

Download data: TXT

(Submitter supplied) Tomato is a major global crop however its production is limited by Botrytis cinerea. Due to the toxicity of post-harvest pesticide application, alternative control methods such as priming are being investigated. Plants were treated with β-aminobutyric (BABA) at two developmental stages and resistance against B. cinerea was tested in fruit tissue and in progenies. DNA methylation and RNA sequencing were conducted to characterise the (epi)genetic changes associated with long-lasting resistance. more...

Organism:

Solanum lycopersicum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27957

24 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis was conducted to elucidate the transcriptome-wide gene expression differences between the wild-type and the slalkbh2 mutants (slalkbh2-25 and slalkbh2-28). In comparison to the wild-type, we identified 602 downregulated genes and 833 upregulated genes in the slalkbh2-25 mutant, as well as 556 downregulated genes and 470 upregulated genes in the slalkbh2-28 mutant (with a cutoff criterion of FPKM fold change ≥ 1.5 and P value < 0.05). more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24124

9 Samples

Download data: TXT

(Submitter supplied) We conducted m6A-seq on the fruits of both wild-type and slalkbh2 mutants (slalkbh2-25 and slalkbh2-28) at the mature green (MG) stage, which represents the onset of fruit ripening, to identify putative SlALKBH2 targets. Approximately 10,000 high-confidence m6A peaks were identified in the fruit samples of wild-type, slalkbh2-25, and slalkbh2-28, predominantly situated near the stop codons and in the 3’ UTR regions of gene transcripts. more...

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL24124

18 Samples

Download data: BW

(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:

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

Type:

Expression profiling by high throughput sequencing

5 related Platforms

49 Samples

Download data: CSV

(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) 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) 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

(Submitter supplied) To investigate the difference of gene expression regulated by JMJ4, we performed RNA-seq assay of jmj4 mutant and wild type plants under control and cold treatment conditions.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

12 Samples

Download data: TXT

(Submitter supplied) To clarify the specific regulating mechanism of JMJ4 under cold treatment, we performed ChIP-seq assay of jmj4 mutant and wild type plants under control and cold treatment conditions.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27957

15 Samples

Download data: BW

(Submitter supplied) We performed iCLIP2 in tomato leaves stably expressing GFP-tagged RS2Z35 or RS2Z36.

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL21762

8 Samples

Download data: BED, BW

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

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL21762

17 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21762

4 Samples

Download data: TXT