GEO DataSets

(Submitter supplied) Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavages by small RNAs. Here we developed an extension module based on a deep learning convolutional neural network (CNN) in a machine learning environment to discriminate false from true cleavage sites applied on datasets from potato (Solanum tuberosum, St) and the oomycete pathogen Phytophthora infestans (Pi). The core of the CNN module is a stochastic gradient descent optimizer with cyclical learning rate (CLR) which together with Bayesian optimization scored a validation accuracy of 100%. more...

Organism:

Solanum tuberosum; Phytophthora infestans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

4 related Platforms

35 Samples

Download data: XLS

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

Organism:

Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19354 GPL19416

16 Samples

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(Submitter supplied) Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. more...

Organism:

Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19416

8 Samples

Download data: FA, TXT

(Submitter supplied) Background: The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. more...

Organism:

Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19354

8 Samples

Download data: TSV

(Submitter supplied) The expression of genes in P. infestans was monitored over a five day time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two days post-inoculation with expression decaying over the five day time course.

Organism:

Solanum lycopersicum; Phytophthora infestans

Type:

Expression profiling by array

Platform:

GPL8093

14 Samples

Download data: TXT

(Submitter supplied) Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). more...

Organism:

Phytophthora infestans; Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29221 GPL19416 GPL22257

13 Samples

Download data: TSV

(Submitter supplied) The expression of genes in P. infestans isolates 06_3928A and NL07434 was monitored from 2 to 4 days time course of a potato infection. Genes encoding known and putative effector proteins were found induced at two and/or three days post-inoculation.

Organism:

Solanum lycopersicum; Phytophthora infestans

Type:

Expression profiling by array

Platform:

GPL8093

20 Samples

Download data: TXT