Gene expression profiling of rice seedlings in response to glutamine treatment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697351", "kind": "science-record", "revision": 6, "content_hash": "sha256:ecba711c5bc52e2dde66ab7c8908f6048274a57b14e36af1dfedda02972df270", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:20:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling of rice seedlings in response to glutamine treatment.", "doi": "10.1016/j.gdata.2015.08.023", "pmid": "26697351", "authors": ["Chia-Cheng Kan", "Tsui-Yun Chung", "Ming-Hsiun Hsieh"], "journal": "Genomics data", "year": 2015, "abstract": "Glutamine, the most abundant free amino acid in humans (Curi et al., 2007 [1]), has many functions. In addition to protein, amino acid, and nucleic acid biosynthesis, glutamine also regulates the expression of genes related to metabolism, cell defense, and signal transduction in humans (Curi et al., 2007 [1]; Brasse-Lagnel et al., 2009 [2]). Glutamine is also one of the major forms of nitrogen in rice (Fukumorita and Chino, 1982 [3]). In addition to metabolic and nutritional effects, glutamine may function as a signaling molecule to regulate gene expression in plants. To this end, we used microarray analysis to identify genes that are rapidly induced by 2.5 mM glutamine in rice roots. The results revealed that glutamine induced the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses within 30 min (Kan et al., 2015 [4]). Here, we provide the details of the experimental procedure associated with our microarray data deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE56770).", "claims": [{"id": "claim-method", "statement": "Unpaired t-tests were performed to examine the reproducibility of the data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697351", "locator": "sections[6] \"Microarray analysis\" paragraph 2", "quote": "Unpaired t-tests were performed to examine the reproducibility of the data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56770.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697351", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56770."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Glutamine rapidly up-regulated the expression of at least 35 genes in rice roots after a 30-minute treatment with 2.5 mM glutamine.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697351", "locator": "sections[6] \"Microarray analysis\" paragraph 2", "quote": "Thus, we concluded that glutamine rapidly up-regulated the expression of at least 35 genes in rice roots [4]."}, {"asset": "source:pmid:26697351", "locator": "sections[6] \"Microarray analysis\" paragraph 2", "quote": "Unpaired t-tests were performed to examine the reproducibility of the data. A two-fold cutoff and a P-value less than 0.05 were applied to select for up- and down-regulated genes after 2.5 mM Gln treatment for 30 min."}, {"asset": "source:pmid:26697351", "locator": "sections[6] \"Microarray analysis\" paragraph 2", "quote": "The scanned arrays were analyzed by Affymetrix GCOS version 1.4 and the raw data were saved as CEL files."}, {"asset": "source:pmid:26697351", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56770."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Glutamine rapidly up-regulated the expression of at least 35 genes in rice roots after a 30-minute treatment with 2.5 mM glutamine.", "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:26697351"], "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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To this end, we used microarray analysis to identify genes that are rapidly", "e experimental procedure associated with our microarray data deposited in NCBI's Gene Expression Omn", "o perform gene expression profiling with the Affymetrix GeneChip Rice Genome Array (Fig. 1). Plant m"], "order_basis": "paper_text_order:631", "id": "assay:1"}]}