Transcriptomic dataset from Arabidopsis thaliana seedlings in response to Pseudomonas aeruginosa mono-rhamnolipids.

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Bacterial rhamnolipids (RLs) are biosurfactant known to trigger plant defense mechanisms and have a great potential for crop culture protection as environmental-friendly biocontrol solution. They are thought to interact directly with membrane lipids to induce plant defense gene expression and protection towards phytopathogens. However, to date, data on the global transcriptomic modifications induced by these natural amphiphilic glycolipids in plants are missing. Ten-day-old seedlings were treated for 1 or 3 h with 100 µM Mono-RLs in liquid growth medium for root absorption. Total RNA samples were extracted, purified, labelled and hybridized to Agilent V4 Gene Expression Microarrays 4 × 44 K (design ID 021169) carrying 43803 ssDNA probes of 60-mer covering the entire genome of A. thaliana. The dataset was validated by quality assessments including RNA sample quality, microarray quality and global gene expression profiling. The raw and normalized formats of these transcriptomic data are available via GEO repository with the accession number GSE168830. The dataset can be used to provide insights into the plant's early and later mechanisms induced or repressed by RLs. It can be compared to data obtained with other plant defense elicitors, including the well described compounds perceived by membrane protein receptors.", "claims": [{"id": "claim-method", "statement": "Processing of the dataset was realized using LIMMA (Linear Models for Microarray and RNA-Seq Data) package version 3.40.6 [5] of the bioconductor project [6] on R software version 3.6.1 [7].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34621928", "locator": "sections[9] \"Data acquisition and analysis\" paragraph 2", "quote": "Processing of the dataset was realized using LIMMA (Linear Models for Microarray and RNA-Seq Data) package version 3.40.6 [5] of the bioconductor project [6] on R software version 3.6.1 [7]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw and normalized formats of these transcriptomic data are available via GEO repository with the accession number GSE168830.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34621928", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw and normalized formats of these transcriptomic data are available via GEO repository with the accession number GSE168830."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34621928"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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