GEO DataSets

(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) The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9). more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL16358

15 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 arcanum; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24124 GPL28683

18 Samples

Download data: FASTA, TAB

(Submitter supplied) Purpose: To understand the molecular mechanisms involved in disease development during plant-nematode interactions. Methods: We have taken a comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in tomato roots at five infection time points from susceptible plants (PR: Pusa Ruby) and two infection time points from resistant plants (M36: Transgenic MM line), grown under soil conditions. more...

Organism:

Solanum lycopersicum; Meloidogyne incognita

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22563

34 Samples

Download data: BW, TAB

(Submitter supplied) Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26062

9 Samples

Download data: TXT

(Submitter supplied) We employed microarray analysis to observe dynamic changes of gene expression profiles in response to mild and severe potato spindle tuber (PSTVd) infection in the roots of tomato cv ‘Rutgers’.

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

26 Samples

Download data: CEL

(Submitter supplied) Plants adjust their growth in response to environmental cues by forming new organs in different development contexts. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root/shoot trajectory separation and generate shoot-borne-roots through an unknown mechanism. Here, we mapped tomato (Solanum lycoperiscum) shoot-borne-roots development at single-cell resolution and show that they initiate from differentiated phloem-associated cells via a unique transitional stem-cell-like state. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29032

1 Sample

Download data: CSV, TXT

(Submitter supplied) The purpose of this dataset is to generate a transcriptomic series of staged non-induced lateral root intiation in M82 tomato. Sections of the primary roots containing lateral roots at 5 different developemental stages (staged by their anatomy and expression of the auxin response marker DR5) were collected.

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21762

12 Samples

Download data: CSV

(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) RKNs are economically most damaging, obligate sedentary endoparasites that form giant cells within host roots to obtain nutrition and complete their life cycle. We report genome-wide identification of miRNAs from both host and RKN using RKN-infected susceptible tomato roots through high-throughput sequencing. Eleven small RNA libraries were made from five disease development stages, their five corresponding uninfected development stages and uninfected development stage 0. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16345

11 Samples

Download data: TXT