GEO DataSets

(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

(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

(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:

Other

Platform:

GPL21762

4 Samples

Download data

(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:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21762

9 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK, TXT

(Submitter supplied) The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive CCaMK via GCC boxes. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

12 Samples

Download data: XLSX

(Submitter supplied) The aim of study is to investigate DEGs, long non-coding RNAs and alternative splicing events in the development of galls and neighboring region compared to the non-infected whole root induced by root-knot nematode (RKN, Meloidogyne incognita). Total RNA was extracted, ribosomal depleted libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovaSeq 6000. High quality, paired-end reads were then aligned to the tomato reference genome (Heinz1706 assembly SL4.0) and uniquely mapped reads were counted using Htseq. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

18 Samples

Download data: XLSX

(Submitter supplied) Assessment of RS2Z protein function under heat stress in Solanum Lycopersicum via RNASeq and iCLIP2. This SuperSeries is composed of the SubSeries listed below.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21762 GPL27957

32 Samples

Download data: BW, TAB