Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants.

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After 21-days of postinoculation, total RNA was extracted and subjected for deep-sequencing using Illumina HiSeq platform. The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data. The filtered sRNA population was then mapped against both the genomic (+) and antigenomic (-) strands of the respective PSTVd variants using standard pattern-matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism. High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.", "claims": [{"id": "claim-data-access", "statement": "High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697336", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using a standard pattern-matching algorithm, the study found that PSTVd-I-infected plants produced more viroid-derived sRNA (11.3%) than PSTVd-M-infected plants (2.3%); the source sequence data are available through GEO accession GSE69225 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69225.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697336", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 4", "quote": "That said, PSTVd-I inoculated plants showed more vd-sRNA (11.3%) than PSTVd-M (2.3%) inoculated plants."}, {"asset": "source:pmid:26697336", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 4", "quote": "All 21- to 24-nt long vd-sRNAs were profiled on both polarity strands of the respective PSTVd variants using the standard pattern-matching algorithm in order to understand the production of the vd-sRNAs (Fig. 1)."}, {"asset": "source:pmid:26697336", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225."}, {"asset": "source:pmid:26697336", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69225."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using a standard pattern-matching algorithm, the study found that PSTVd-I-infected plants produced more viroid-derived sRNA (11.3%) than PSTVd-M-infected plants (2.3%); the source sequence data are available through GEO accession GSE69225 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69225.", "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:26697336"], "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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