Dataset of protein changes induced by cold acclimation in red clover (Trifolium pratense L.) populations recurrently selected for improved freezing tolerance.

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Proteins were extracted from crowns of two red clover cultivars grown under non-acclimated or cold-acclimated conditions, and plants obtained from the initial genetic background (TF0) and from populations obtained after three (TF3) and four cycles (TF4) of recurrent selection for superior freezing tolerance. Proteins were analyzed using a two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled to mass spectroscopy (MS and MS/MS). Differentially regulated proteins were subsequently identified using MALDI TOF/TOF analysis. The data are related to a recently published research article describing proteome composition changes associated with freezing tolerance in red clover, \"A proteome analysis of freezing tolerance in red clover (Trifolium pratense L.)\" (Bertrand et al., 2016 [1]). They are available in the ProteomeXchange Consortium database via the PRIDE partner repository under the dataset identifier PRIDE: PXD003689.", "claims": [{"id": "claim-method", "statement": "For each protein spot, changes in abundance in response to cold acclimation and recurrent selection were tested by one-way and two-way ANOVA combined with a Student׳s t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27408927", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "For each protein spot, changes in abundance in response to cold acclimation and recurrent selection were tested by one-way and two-way ANOVA combined with a Student׳s t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are within this article and available via the PRIDE partner repository on the ProteomeXchange Consortium database under the dataset identifier PRIDE: PXD003689.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27408927", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data are within this article and available via the PRIDE partner repository on the ProteomeXchange Consortium database under the dataset identifier PRIDE: PXD003689."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used one-way and two-way ANOVA combined with Student’s t-test to identify differentially regulated proteins, and the source data are available through the PRIDE partner repository under PRIDE: PXD003689.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27408927", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "The average values of four biological replicates (1 rep=1 pot, 10 plants per pot) were used to compare the protein abundances between different treatments."}, {"asset": "source:pmid:27408927", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "For each protein spot, changes in abundance in response to cold acclimation and recurrent selection were tested by one-way and two-way ANOVA combined with a Student׳s t-test."}, {"asset": "source:pmid:27408927", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "Spots with P-values ≤0.01 in ANOVA and t-test and fold changes ratios ≥|1.5| were considered to be differentially regulated."}, {"asset": "source:pmid:27408927", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "They are available in the ProteomeXchange Consortium database via the PRIDE partner repository under the dataset identifier PRIDE: PXD003689."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper used one-way and two-way ANOVA combined with Student’s t-test to identify differentially regulated proteins, and the source data are available through the PRIDE partner repository under PRIDE: PXD003689.", "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:27408927"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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