GEO DataSets

(Submitter supplied) To determine which genes were directly regulated by SlWRKY33 under cold stress, we performed ChIP-seq of SlWRKY33-OE plants with and without cold treatment.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27957

4 Samples

Download data: BW, FA

(Submitter supplied) Transcriptomics study which main goal is to elucidate the programme of gene expression triggered by water stress in leaflets of the drought-tolerant wild-related tomato Solanum pennellii (acc. PE47) compared with domesticated tomato (S. lycopersicum, cv. P73). In this study we used S. lycopersicum (Sl) (cv. P73) and S. pennellii (Sp) (acc. PE47) species displaying remarkable divergences regarding drought tolerance, to investigate the physiological and molecular responses in leaves of plants grown without stress (control) and after four days of water withholding (water stress, WS), when plant water loss was significant but leaves did not show visual dehydration symptoms yet. more...

Organism:

Solanum lycopersicum; Solanum pennellii

Type:

Expression profiling by array

Platform:

GPL4741

12 Samples

Download data: CEL

(Submitter supplied) Tomato is one of the most important crops for human consumption. Unfortunately, its production is affected by diseases caused by pathogens such as the actynomicete Clavibacter michiganensis subsp. michiganens (Cmm). This pathogen is the causal agent of the bacterial canker of tomato, considered one of the most devastating tomato diseases. To date, there are not resistant varieties of commercial tomato against Cmm. more...

Organism:

Solanum lycopersicum; Solanum arcanum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28683 GPL24124

18 Samples

Download data: FASTA, TAB

(Submitter supplied) Cyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (Ailsa Craig variety) and dgt tissues from three spatially separated developmental stages of the root tip (differentiation zone, elongation zone, and meristem), with three replicates for each tissue and genotype.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16345

18 Samples

Download data: TXT

(Submitter supplied) In order to find the specific promoter of tomato exocarp, we extracted RNA extraction from the red ripe exocarp, red ripe mesocarp, mature green exocarp, mature green exocarp and leaf cells, and then performed RNA seq to find the differential genes from the Transcriptome data. Our data provides gene expression data for three tissues of tomato during the red ripe and mature green stages, laying the foundation for the search for differential genes

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27957

10 Samples

Download data: TXT

(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

Platform:

GPL21762

79 Samples

Download data: BIGWIG, NARROWPEAK, TXT

(Submitter supplied) We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. We performed gene expression profiling analysis using data obtained from RNA-seq of 4 weeks old tomato (Solanum lycopersicum cv. Moneymaker background ) plants (wild type and RNAi knock-down lines) which were treated at 45°C for 0h, 1h and 6h.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21762

18 Samples

Download data: TXT

(Submitter supplied) We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To confirm that the temperature and timing used for the heat stress are relevant, we generated RNA-seq data and analyzed changes in gene expression induced by the heat stress treatment.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21762

6 Samples

Download data: TXT

(Submitter supplied) We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To validate the presence of transcription factories we performed a HiChIP experiment, which is a sensitive and efficient method to analyze protein-centric chromosome conformation, using an anti-RNA polymerase II antibody.

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL21762

2 Samples

Download data: TXT

(Submitter supplied) We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To map the three-dimensional chromatin interactions we performed in situ Hi-C, a genome-wide method that detects DNA-DNA physical interactions.

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL21762

6 Samples

Download data: TXT

(Submitter supplied) We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. We performed Amplified DNA affinity purification sequencing assay to determine HSFA1a binding sites.

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL21762

3 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) To investigate the HSFA1a, a master regulator of heat stress response, plays a key role in this reorganization by promoting the formation of promoter/enhancer chromatin loops. To determine if a typical chromatin signature could differentiate distal and proximal REs, we performed ChIP-seq experiments and analyzed the levels of four histone covalent modifications that are permissive for transcription: H3K4me3, H3K9ac, H3K18ac and H3K27ac at 0, 1 and 6 hours after heat stress on both proximal and distal REs specifically active at 1 hour after HS. more...

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21762

32 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To determine whether distal REs come into contact with promoters, instead of using a classical Hi-C, we further combined Hi-C with a capture enrichment step. We generated a biotinylated RNA bait library specifically targeting 212,735 promoter regions and performed a capture Hi-C after 0h, 1h and 6h after stress.

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL21762

6 Samples

Download data: TXT

(Submitter supplied) We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. We performed ATAC-seq experiments which provide accessible chromatin sites that can be used to identify putative regulatory elements coming in physical contact with promoters when they are actived.

Organism:

Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21762

6 Samples

Download data: BIGWIG