GEO DataSets

(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) Comparative analysis of gene expression in tomato leaves 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 leaves of tomato cv ‘Rutgers’.

Organism:

Solanum lycopersicum

Type:

Expression profiling by array

Platform:

GPL4741

35 Samples

Download data: CEL

(Submitter supplied) 5′ RNA ligase mediated rapid amplification of cDNA ends (5′ RLM-RACE) is the widely used tool for confirming the direct cleavage of target mRNA by a miRNA. Recently, 5′ RLM-RACE combined with high-throughput sequencing such as parallel analysis of RNA ends (PARE) are gaining importance as these techniques allows to assess the large number of sample in a single experiment. In order to verify the cleavage of predicted a target mRNA in potato spindle tuber viroid (PSTVd) infected tomato plants, the the leaf samples collected from the mock inoculated (control/healthy) at 21-days were subjected for RNA extraction. more...

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL20585

1 Sample

Download data: XLSX

(Submitter supplied) In order to compare the small RNA (sRNA) population between the control and Potato spindle tuber viroid (PSTVd) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were mock inoculated. At 21 dpi,tTotal RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20585

1 Sample

Download data: XLSX

(Submitter supplied) In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid- RG1 strain (PSTVd-RG1) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-RG1. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

Organism:

Potato spindle tuber viroid

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20595

1 Sample

Download data: TXT

(Submitter supplied) In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid-intermediate strain (PSTVd-I) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-I. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

Organism:

Potato spindle tuber viroid

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20595

1 Sample

Download data: TXT

(Submitter supplied) 5′ RNA ligase mediated rapid amplification of cDNA ends (5′ RLM-RACE) is the widely used tool for confirming the direct cleavage of target mRNA by a miRNA. Recently, 5′ RLM-RACE combined with high-throughput sequencing such as parallel analysis of RNA ends (PARE) are gaining importance as these techniques allows to assess the large number of sample in a single experiment. In order to validate the cleavage of predicted a target mRNA in potato spindle tuber viroid-RG1 (PSTVd-RG1) infected tomato plants, the leaf samples collected at 21-days post inoculation were subjected for RNA extraction. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20585

1 Sample

Download data: XLSX

(Submitter supplied) 5′ RNA ligase mediated rapid amplification of cDNA ends (5′ RLM-RACE) is the widely used tool for confirming the direct cleavage of target mRNA by a miRNA. Recently, 5′ RLM-RACE combined with high-throughput sequencing such as parallel analysis of RNA ends (PARE) are gaining importance as these techniques allows to assess the large number of sample in a single experiment. In order to validate the cleavage of predicted a target mRNA in viroid infected tomato plants, the leaf samples collected at 21-days post inoculation were subjected for RNA extraction. more...

Organism:

Solanum lycopersicum

Type:

Other

Platform:

GPL20585

1 Sample

Download data: XLSX

(Submitter supplied) In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15580

3 Samples

Download data: TXT

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

Organism:

Nicotiana benthamiana; Solanum lycopersicum; Nicotiana tabacum

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL21056 GPL24943

24 Samples

Download data: TXT

(Submitter supplied) Viruses have different strategy to infect their hosts. Acute type infection is fast resulting in severe symptoms or in the death of the plant, while in persistent type of interaction the virus can survive within its host for a long period of time with mild symptoms. During our studies we investigated gene expression changes of virus infected Nicotiana benthamiana and Solanum lycopersicum after systemic spread of the virus by two different methods: microarray hybridization and RNA sequencing. more...

Organism:

Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24943

12 Samples

Download data: DIFF, TXT

(Submitter supplied) Viruses have different strategy to infect their hosts. Acute type infection is fast resulting in severe symptoms or in the death of the plant, while in persistent type of interaction the virus can survive within its host for a long period of time with mild symptoms. During our studies we investigated gene expression changes of virus infected Nicotiana benthamiana and Solanum lycopersicum after systemic spread of the virus by two different methods: microarray hybridization and RNA sequencing. more...

Organism:

Nicotiana benthamiana; Nicotiana tabacum

Type:

Expression profiling by array

Platform:

GPL21056

12 Samples

Download data: TXT

(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