Genome-wide analysis of uncapped mRNAs under heat stress in Arabidopsis.

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One of the primary functions of these mRNP complexes is mRNA decay, which generates uncapped mRNAs by the action of endonucleases and decapping enzymes (Thomas et al., 2011) [1]. In order to figure out whether TSN proteins could be implicated in mRNA decay, we isolated uncapped and total mRNAs of Wild type (WT; Col and Ler) and TSN double knock-out (tsn1tsn2) seedlings grown under heat stress (39 °C for 40 min) and control (23 °C) conditions. Here, we provide the experimental procedure to reproduce the results (NCBI GEO accession number GSE63522) published by Gutierrez-Beltran et al. (2015) in The Plant Cell [2].", "claims": [{"id": "claim-method", "statement": "The samples were normalized using the ranked median quantiles as described previously [5].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484210", "locator": "sections[6] \"Microarray analysis\" paragraph 2", "quote": "The samples were normalized using the ranked median quantiles as described previously [5]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used ranked median quantiles for microarray normalization and provides the raw and processed source data through GEO accession GSE63522 and its direct GEO link.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484210", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we provide the experimental procedure to reproduce the results (NCBI GEO accession number GSE63522) published by Gutierrez-Beltran et al. (2015) in The Plant Cell [2]."}, {"asset": "source:pmid:26484210", "locator": "sections[6] \"Microarray analysis\" paragraph 2", "quote": "The samples were normalized using the ranked median quantiles as described previously [5]."}, {"asset": "source:pmid:26484210", "locator": "sections[6] \"Microarray analysis\" paragraph 2", "quote": "The normalized data are included within GSM1551500-23 table."}, {"asset": "source:pmid:26484210", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63522."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used ranked median quantiles for microarray normalization and provides the raw and processed source data through GEO accession GSE63522 and its direct GEO link.", "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:26484210"], "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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