GEO DataSets

(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:

Arabidopsis thaliana; Solanum lycopersicum; Zea mays; Oryza sativa

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 x Solanum pennellii; Solanum lycopersicum

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

(Submitter supplied) To investigate the role of Serine/Arginine-rich proteins RS2Z35 and RS2Z36 in tomato heat stress response and thermotolerance, we established single and double knockouts of the respective splicing factor(s) in tomato We then performed gene expression and splicing analysis using data obtained from RNA-seq of wildtype, single knockout and double knockout plants under control and heat stress conditions (1 h 40°C)

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

24 Samples

Download data: TAB

(Submitter supplied) To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28981

9 Samples

Download data: TSV

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21762

4 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21762

4 Samples

Download data: BIGWIG

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

Organism:

Solanum lycopersicum

Type:

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

Platforms:

GPL27957 GPL21762

47 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

6 Samples

Download data: TXT

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL21762

5 Samples

Download data: TXT