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SRP092151
Arabidopsis thaliana
9 Downloadable Samples
Illumina HiSeq 2000
Description
The study aims to identify differences in gene expression in the root tissue of wild type Columbia-0 as well as Arabidopsis Mediator subunit mutants, med18 and med20 in response to the root pathogen Fusarium oxysporum. Roots were inoculated for 24 hours before harvesting for RNA isolation and paired end Illumina sequencing.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Disease stage, Treatment
View Samples- Triticum aestivum
- 111 Downloadable Samples
Affymetrix Wheat Genome Array (wheat)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identification of biomarker genes for resistance to a pathogen by a novel method for meta-analysis of single-channel microarray datasets.
Sample Metadata Fields
Specimen part
View Samples- Triticum aestivum
- 90 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Triticum aestivum
- 77 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 39 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material identified 1,327 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. A sub-set of 378 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present.
Publication Title
Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci.
Sample Metadata Fields
No sample metadata fields
View Samples- Triticum aestivum
- 76 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci.
Sample Metadata Fields
No sample metadata fields
View Samples- Triticum aestivum
- 72 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 36 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material in location 2 identified 10,280 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. Of these 1,455 were identified in the point location as well. A sub-set of 542 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present.
Publication Title
Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci.
Sample Metadata Fields
No sample metadata fields
View Samples- Triticum aestivum
- 46 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes) and developing seeds. This study compares the gene expression profile of heads from the susceptible cultivar Roblin after inoculation with either water (W) or the disarmed Fg strain tri6 (T6). Tri6 is a global transcription regulator affecting the trichothecene biosynthesis pathway.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Triticum aestivum
- 32 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes) and developing seeds. This study compare the gene expression profile in wheat spikelets (spk 2) inoculated with either water (mock treatment) or a pathogenic strain of Fusarium graminearum (WT); spikelets 2 were inoculated 24 hrs after a neighbour spikelet (spk 0) was treated with either water or F. graminerum mutant strain Tri6 or NoxAB. Spikelets 2 were sampled 8 and 24 hrs after the second treatment.
Publication Title
Components of priming-induced resistance to Fusarium head blight in wheat revealed by two distinct mutants of Fusarium graminearum.
Sample Metadata Fields
Specimen part
View Samples- Triticum aestivum
- 30 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes). This study compare the gene expression profile in wheat spikelets from near isogenic spring wheat lines carrying or not the FHB resistance QTL 2DL, after inoculation with water (H2O) or Fg; two inoculation methods were also compared, point and spray inoculation.
Publication Title
Identification of biomarker genes for resistance to a pathogen by a novel method for meta-analysis of single-channel microarray datasets.
Sample Metadata Fields
Specimen part
View Samples- Phytophthora sojae, Glycine max
- 14 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
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.
Publication Title
The Phytophthora sojae avirulence locus Avr3c encodes a multi-copy RXLR effector with sequence polymorphisms among pathogen strains.
Sample Metadata Fields
Specimen part, Time
View Samples