Ontology highlight
ABSTRACT:
PROVIDER: PRJNA641250 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12072914_1.fastq.gz | Fastqsanger.gz | |||
| SRR12072914_2.fastq.gz | Fastqsanger.gz | |||
| SRR12072915_1.fastq.gz | Fastqsanger.gz | |||
| SRR12072915_2.fastq.gz | Fastqsanger.gz | |||
| SRR12072916_1.fastq.gz | Fastqsanger.gz |
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Project description:Cereal aphids can successfully colonize and damage switchgrass (Panicum virgatum) plants. Among the aphids tested, greenbugs (Schizaphis graminum, GB) caused significant plant damage likely through a combination of aphid-salivary proteins that are injected into plants during feeding and a strong host response elicited by herbivory. In this study, changes in protein phosphorylation present in GB-infested and uninfested control plants was determined. These data were compared against transcriptome changes recently published for this system.
2022-02-04 | PXD018546 | Pride
Project description:Cereal aphids can successfully colonize and damage switchgrass (Panicum virgatum) plants. Among the aphids tested, greenbugs (Schizaphis graminum, GB) caused significant plant damage likely through a combination of aphid-salivary proteins that are injected into plants during feeding and a strong host response elicited by herbivory. In this study, shotgun label-free proteomics has been used to document changes to the switchgrass proteome as a result of GB infestation. These proteomic data were compared against transcriptome changes recently published for this system.
2022-02-04 | PXD018547 | Pride
Project description:Cd levels in the shoots, as well as in the roots were unexpectedly reduced in 35S:AtHMA4-expressing tobacco. Obtained results indicate that in the generation of the Cd-related phenotypes of transgenic plants substantial modifications of the host plant transcriptome was involved. Microarray based analysis was performed to compare expression profiles of the roots from tobacco expressing 35S-AtHMA4 with the wild-type (WT) plants, which were grown in the presence of 0.25 µM Cd. An effort was undertaken to understand which processes were modified in tobacco as a result of the expression of 35S:AtHMA4, which lead to decreased Cd uptake and lower accumulation in the shoots. Knowing underlying mechanisms is important for developing strategies to grow low cadmium tobacco.
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Project description:Transcriptome analysis in tobacco mutant plants using tomato Genechip Genome array Tobacco (Nicotiana tabacum cv. Petit Havanna) psaA and psbA deletion mutants were constructed through a targeted deletion of 767 and 1152 nucleotides of coding regions, respectively with two gene cassettes: psbAproR:uidA:psbterR and rrnR:aadA:rbcLterR coding for GUS reporter and spectinomycin selectable marker genes, respectively. Standard established procedures were followed for chloroplast transformation to generate the psaA and psbA deletion mutants based on the homologous recombination. Gene expression profiles in psaA and psbA tobacco mutant plants were analyzed using tomato Genechip Genome array to study the global changes in the expression of genome.
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Project description:Response of the aphid head transcriptome to nicotine in artificial diets (250 µM nicotine, 24 hours feeding) Two condition experiment: heads of aphids feeding on control diet vs heads of aphids feeding on 250 µM nicotine containing diet
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Project description:Response of the aphid head transcriptome to nicotine in artificial diets (100 µM nicotine, 24 hours feeding) Two condition experiment: heads of aphids feeding on control diet vs heads of aphids feeding on 100 µM nicotine containing diet
2010-05-14 | E-GEOD-18657 | biostudies-arrayexpress
Project description:Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. Aphids do not normally kill their host and colonize plants for long periods of time, up to several months in soybean. However, our knowledge of plant responses to long-term aphid colonization is very limited. We used microarrays to characterize the soybean plant's transcriptional response against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured transcript levels in leaves after 21 days of aphid infestation.
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Project description:Reference: De Vos and Jander, 2009 - Plant, Cell, and Environment Aim: Identification of genes responding to aphid saliva. Background: During feeding on phloem sap aphids repeatedly salivate into the sieve element. It is thought that compounds in aphid saliva play a role in sustainable feeding. These compounds may include proteins and small molecules, which can function as virulence factors. Growth conditions Plants: Seeds of wild-type Arabidopsis thaliana (Col-0) were obtained from the were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix with Osmocoat fertilizer. Plants were grown in Conviron growth chambers in 20- x 40-cm nursery flats at a photosynthetic photon flux density of 200 mmol m-2 s-1 and a 16-h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. Plants were grown for 3 weeks and used in experiments before flowering. Aphids: All experiments were conducted with a tobacco-adapted red lineage of M. persicae. Aphids were raised on cabbage (Brassica oleracea) with a 16-h day (150 mmol m-2 s-1 at 24°C) and an 8-h night (19°C) at 50% relative humidity. Experimental set-up/treatment: Fifty aphids were allowed to feed from 50 µL artificial diet, containing sucrose and amino acids (Kim and Jander, 2007) between two layers of Parafilm. After 24 h, artificial diet from 20 aphids and control (0 aphids) diet cups was collected and infiltrated into leaves of intact Arabidopsis plants using a 1-mL syringe without the needle. Plants for control diet and aphid saliva containing diet were grown in the same pot to allow for a paired comparison. Eighteen leaves (3 leaves from 6 plants) treated with control and aphid saliva containing diet were harvested and immediately frozen in liquid nitrogen. This experiment was repeated 3 times to function as independent biological replicates. RNA extraction + processing: RNA was extracted using the Qiagen Plant RNeasy kit. RNA quality and quantity was assessed with an Agilent BioAnalyser 2100. Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Data analysis: Raw data from the microarrays was normalized at probe-level using gcRMA algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system. Significance of gene expression was determined using the LIMMA (Smyth, 2004) program and raw p values of multiple tests were corrected using False Discovery Rate (FDR).
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Project description:Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were fed six different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness. Science for Life Laboratory (SciLifeLab, Sweden) conducted the sequencing of RNA samples. The cDNA libraries (Illumina TruSeq RNA) were sequenced using the Illumina HiSeq 2000 platform using 100-bp paired-end sequencing. We obtained more than 9 million read-pairs from seventy one cDNA libraries sequenced and the transcriptome assembly (TA) of these sequences resulted in 213, 237 transcripts (162,189 components) with a contig N50 of 2,193 bp. Thus, we covered approximately 300x the transcriptome of caterpillars of the species V. cardui.
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Project description:Transcriptome analysis in tobacco mutant plants using tomato Genechip Genome array Tobacco (Nicotiana tabacum cv. Petit Havanna) psaA and psbA deletion mutants were constructed through a targeted deletion of 767 and 1152 nucleotides of coding regions, respectively with two gene cassettes: psbAproR:uidA:psbterR and rrnR:aadA:rbcLterR coding for GUS reporter and spectinomycin selectable marker genes, respectively. Standard established procedures were followed for chloroplast transformation to generate the psaA and psbA deletion mutants based on the homologous recombination. Gene expression profiles in psaA and psbA tobacco mutant plants were analyzed using tomato Genechip Genome array to study the global changes in the expression of genome. Total RNA was isolated from psaA and psbA tobacco mutant plants along with the wild type plants. Biotin labeled cRNA was hybridized on tomato GeneChip Genome Array following the Affymetrix protocols. Two independent biological replicates were maintained.
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