GEO DataSets

(Submitter supplied) Plant pathogens secreted effector proteins to overcome host immunity system and gain access to colonization. Although more than 300 hundred of RxLR effectors were encoded by the devastating soybean pathogen Phytophthora sojae, the patterns of conditionally expressed effector genes were well programmed. However, the effector gene regulation mechanisms were not fully dissected. In this study, we identified the H3K36me3 methyltransferase PsKMT3. more...

Organism:

Phytophthora sojae strain P6497

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32312

10 Samples

Download data: CSV

(Submitter supplied) Plant pathogens secreted effector proteins to overcome host immunity system and gain access to colonization. Although more than 300 hundred of RxLR effectors were encoded by the devastating soybean pathogen Phytophthora sojae, the patterns of conditionally expressed effector genes were well programmed. However, the effector gene regulation mechanisms were not fully dissected. In this study, we identified the H3K36me3 methyltransferase PsKMT3. more...

Organism:

Phytophthora sojae strain P6497

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32311

7 Samples

Download data: BW

(Submitter supplied) Hypocotyls of soybean (Glycine max) seedlings of cultivar Williams were inoculated with mycelia of the oomycete pathogen Phytophthora sojae grown in liquid V8 medium or the hypocotyls were mock inoculated. After 12 hours, the sites of inoculation were excised from the hypocotyls and frozen for RNA extraction. Phytophthora sojae mycelia used for inoculation was saved for RNA extraction also

Organism:

Glycine max; Phytophthora sojae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30549 GPL30550 GPL30548

20 Samples

Download data: XLSX

(Submitter supplied) Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromeric sequences are diverse and usually repetitive across species, making them challenging to assemble and identify. Here, we describe centromeres in the model oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). more...

Organism:

Phytophthora sojae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25217

3 Samples

Download data: BW

(Submitter supplied) Purpose and methods:Transcriptome profiling of Phytophthora sojae pssu(z)12 mutant T34 (lost 561bp by CRISPR/Cas9) mycelium (3-days old) were generated to find out the relationship between H3K27me3 and gene expression on Avr1b locus. Wild-type P. sojae P6497 was took as a comparative control. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiles were displayed using IGV browser.

Organism:

Phytophthora sojae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25217

2 Samples

Download data: GTF, XLSX

(Submitter supplied) We report the H3K27me3 profile on Avr1b locus in two Phytophthora sojae strains P6497 and pssu(z)12 mutant. Nuclei of Phytophthora sojae P6497 and pssu(z)12 mutant T34 (lost 561bp by CRISPR/Cas9) mycelium (3-days old) was extracted and digested to 200-400bp using micrococcal nuclease (MNase: NEB M0247S). The antibody Millipore 07-449 was used to immunoprecipitation. We find significant accumulation of H3K27me3 at Avr1b locus in Avr1b silencing strain P6497 and clear H3K27me3 depletion at Avr1b locus in Avr1b unsilenced strain pssu(z)12 mutant T34.

Organism:

Phytophthora sojae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25217

9 Samples

Download data: BW

(Submitter supplied) Purpose and methods:Transcriptome profiling of Phytophthora sojae P6497 mycelium (3-days old) and Phytophthora infestans T30-4 mycelium (6-days old) were generated to find out the relationship between 6mA methylation and gene expression. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiling of P. sojae psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was generated to check the differential expressed genes (DEGs) between the mutant and wild-type P. more...

Organism:

Phytophthora infestans; Phytophthora sojae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25218 GPL25217

7 Samples

Download data: GTF, XLSX

(Submitter supplied) We report the 6mA methylation profiling in two Phytophthora species and one psdamt3 mutant. Genomic DNA of Phytophthora sojae P6497 mycelium (3-days old), Phytophthora infestans T30-4 mycelium and psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was extracted and sonicated to 200-400bp using Biorupter UCD-600. The antibody sysy 202003 was used to immunoprecipitation. We find that 6mA is associated with lowly expressed genes in two Phytophthora species. more...

Organism:

Phytophthora infestans; Phytophthora sojae

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL25217 GPL25218

12 Samples

Download data: BED

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

Organism:

Phytophthora infestans; Phytophthora sojae; Phytophthora ramorum

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17596 GPL17597 GPL17598

4 Samples

Download data: GFF3

(Submitter supplied) Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. more...

Organism:

Phytophthora sojae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17598

1 Sample

Download data: GFF3

(Submitter supplied) The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 10 different developmental and infection stages based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. more...

Organism:

Glycine max; Phytophthora sojae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13671 GPL13672

10 Samples

Download data

(Submitter supplied) Total RNA extracted from Phytophthora sojae (strain P6497) and infected soybean hypocotyls (cultivar Harosoy) provided template for synthesis of cDNA probes used in the microarray hybridizations. Infected plant hypocotyls were sampled 6 h, 12 h, 24 h, and 48 h after inoculation. Mycelia were grown on synthetic media (H&S) or vegetable juice media (V8). Zoospores were sampled at 0 h, 2 h and 6 h after inducing encystment and germination by agitation. more...

Organism:

Phytophthora sojae; Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

28 Samples

Download data: CEL, CHP