Ontology highlight
ABSTRACT:
PROVIDER: PRJNA552611 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9643430.fastq.gz | Fastqsanger.gz | |||
| SRR9643431.fastq.gz | Fastqsanger.gz | |||
| SRR9643432.fastq.gz | Fastqsanger.gz | |||
| SRR9851950.fastq.gz | Fastqsanger.gz | |||
| SRR9851960.fastq.gz | Fastqsanger.gz |
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Project description:The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and during poplar leaf infection. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and development stages. Another goal was to monitor gene expression profiles during poplar leaf infection and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses.
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Project description:To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChip® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Keywords: genetic modification, stress response
2009-08-01 | GSE16419 | GEO
Project description:To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChip® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Keywords: genetic modification, stress response
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Project description:We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages.
2010-06-15 | GSE21868 | GEO
Project description:We aim to understand the global transcriptional response of hybrid poplar NM6 (Populus nigra x Populus maximoviczii) to infection by two biotrophic Melampsora fungi, M. larici-populina and M. medusae f. sp. deltoidae separately and simultanously. Transcript profilling revealed 699 differentially expressed genes whose expression level was equal or higher than 2-fold between infected and noninfected tissues. In the mixed infection, our results showed an additive response of the two pathogens. Genes regulated as a result of Melampsora infection were generally induced and mainly involved in primary/secondary metabolism that include cell wall reinforcement and lignification, defense-related processes like pathogenesis-related and stress response, signal perception and transduction mechanisms and regulation of transcription. Keywords: Stress response
2008-11-22 | GSE9673 | GEO
Project description:The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and infected Poplar leaves. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and development stages. Another goal was to monitor gene expression at different developmental stages and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses. We performed 9 hybridizations (Nimblegen) with samples derived from urediniospores, germlings and infected Poplar leaves (three replicates each). Samples from infected leaves were harvested 96 hours post infection. All samples were labeled with Cy3.
2011-04-30 | E-GEOD-23097 | biostudies-arrayexpress
Project description:To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChip® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Experiment Overall Design: Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization to Affymetrix GeneChips®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChips® were used in this study. Data for the WRKY23-overexpressor plants were processed separately from the data for the Mmt-inoculated WRKY23-RNAi plants. The raw data for the Mmt-inoculated wildtype plants were the same in both cases. Experiment Overall Design: This part of the study includes 12 RNA samples consisting of three biological replicates for each of the mock-inoculated or Mmt-inoculated WT and WRKY23-overexpressing plants.
2009-08-09 | E-GEOD-16417 | biostudies-arrayexpress
Project description:To investigate the function of poplar WRKY23, we generated PtWRKY23-overexpressing and -underexpressing (RNAi) plants. Transgenic plants were inoculated with Melampsora rust or mock-inoculated for assessment of rust-resistance and for gene expression profiling using the poplar Affymetrix GeneChip® to study the consequences of PtWRKY23 overexpression and underexpression. Transcriptome analysis of PtWRKY23 overexpressors revealed a significant overlap with the Melampsora-infection response. Transcriptome analysis also indicated that PtWRKY23 affects redox homeostasis and cell wall-related metabolism. Experiment Overall Design: Leaf discs from wildtype, WRKY23-overexpressor and WRKY23-RNAi plants were inoculated with Melampsora medusae f. sp. tremuloidae (Mmt) or were mock-inoculated (control). At five days post-inoculation, tissues were harvested for RNA extraction and hybridization on Affymetrix GeneChips®. Three biological replications were performed for each line and each inoculation or mock-inoculation. A total of 15 Affymetrix GeneChips® were used in this study. Data for the Mmt-inoculated WRKY23-RNAi plants were processed separately from the data for the WRKY23-overexpressor plants. The raw data for the Mmt-inoculated wildtype plants were the same in both cases. Normalized data for the Mmt-inoculated wildtype plants that were processed with the Mmt-inoculated WRKY23-RNAi plants are denoted with an "a" suffix. Experiment Overall Design: This part of the study includes 6 RNA samples consisting of three biological replicates for the Mmt-inoculated WT and WRKY23-RNAi (underexpressing) plants.
2009-08-09 | E-GEOD-16419 | biostudies-arrayexpress