Transcriptomic dataset of Malus domestica young leaves in response to acibenzolar-S-methyl (ASM) and/or nitrogen nutrition.

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We addressed this question in apple (Malus domestica) by generating a transcriptomic data set of young leaves from seedlings grown in subirrigation systems allowing variations in nitrate supply as the sole nitrogen source. Plants under three contrasting N status (high; limited for 10 days; or just resupplied after a 12 days limitation) received foliar applications of the chemical elicitor acibenzolar-S-methyl (ASM), a functional analog of salicylic acid, or water. Two days later, the youngest developed leaves were sampled for total RNA extraction and sequencing analysis (RNAseq). The current dataset includes 1) a detailed protocol of plant sample production and 2) transcriptomic profile description of young leaves as normalized counts obtained from sequence mapping against the Malus domestica GDDH13v1.1 reference transcriptome. The raw data files and processed data are available at the Gene Expression Omnibus (GEO) repository under the accession number GSE264541. This dataset is a valuable resource to investigate further the molecular mechanisms underlying the role of nitrogen and/or ASM treatment in Malus domestica.", "claims": [{"id": "claim-method", "statement": "RNA-seq libraries were normalized using the TMM (Trimmed Mean of the M-values) method implemented in the R package DeSeq2 [11] (https://cran.r-project.org/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39100780", "locator": "sections[10] \"RNA sequencing and data processing\" paragraph 2", "quote": "RNA-seq libraries were normalized using the TMM (Trimmed Mean of the M-values) method implemented in the R package DeSeq2 [11] (https://cran.r-project.org/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Transcriptomic data from Malus domestica response to Acibenzolar-S-Methyl (ASM) treatment and nitrogen limitation or resupply (Original data) (GEOmnibus).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39100780", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "Transcriptomic data from Malus domestica response to Acibenzolar-S-Methyl (ASM) treatment and nitrogen limitation or resupply (Original data) (GEOmnibus)."}], "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:39100780"], "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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