Dataset for transcriptome and physiological response of mature tomato seed tissues to light and heat during fruit ripening.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33409343", "kind": "science-record", "revision": 8, "content_hash": "sha256:21c3b8aa8cf6d09c6943faacec4d79f7f8b5e23e28cef276d100eb5dc4465669", "created_at": "2026-11-01T15:41:21Z", "updated_at": "2026-11-01T22:45:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dataset for transcriptome and physiological response of mature tomato seed tissues to light and heat during fruit ripening.", "doi": "10.1016/j.dib.2020.106671", "pmid": "33409343", "authors": ["Elise Bizouerne", "Benoit Ly Vu", "Joseph Ly Vu", "Jerome Verdier", "Julia Buitink", "Olivier Leprince"], "journal": "Data in brief", "year": 2021, "abstract": "Seed vigor is an estimate of how successfully a seed lot will establish seedlings under a wide range of environmental conditions, with both the embryo and the surrounding endosperm playing distinct roles in the germination behaviour. Germination and seedling establishment are essential for crop production to be both sustainable and profitable. Seed vigor traits are sequentially acquired during development via genetic programs that are poorly understood, but known to be under the strong influence of environmental conditions. To investigate how light and temperature have an impact on the molecular mechanisms governing seed vigor at harvest, RNA sequencing was performed on Solanum lycopersicum cv. Moneymaker seed tissues (i.e. embryo and endosperm) that were dissected from fruits that were submitted to standard or high temperature and/or standard or dim light. The dataset encompassed a total of 26.5 Gb raw data from mature embryo and endosperm tissues transcriptomes. The raw and mapped reads data on build SL4.0 and annotation ITAG4.0 are available under accession GSE158641 at NCBI Gene Expression Omnibus (GEO) database. Data on seed vigor characteristics are presented together with the differentially expressed gene transcripts. GO and Mapman annotations were generated on ITAG4.0 to analyse this dataset and are provided for datamining future datasets.", "claims": [{"id": "claim-method", "statement": "Number of DEGs were identified using the DEseq2 algorithm with a Benjamini-Hochberg p-value adjustment threshold set at 0.05 to control false positive rate.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33409343", "locator": "sections[3] \"Data Description\" paragraph 7", "quote": "Number of DEGs were identified using the DEseq2 algorithm with a Benjamini-Hochberg p-value adjustment threshold set at 0.05 to control false positive rate."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw and mapped reads data on build SL4.0 and annotation ITAG4.0 are available under accession GSE158641 at NCBI Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33409343", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw and mapped reads data on build SL4.0 and annotation ITAG4.0 are available under accession GSE158641 at NCBI Gene Expression Omnibus (GEO) database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33409343"], "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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Percentages and speed of germination."], ["Parameters for data collection", "Total RNA was extracted from isolated embryo and endosperm tissues of mature Solanum lycopersicum (cv Money Maker) seeds that were harvested at 70 days after flowering (DAF) from fruits that were ripened ex planta from the breaker stage (63 DAF) onwards under standard temperature (23 °C day/ 20 °C night) or high temperature (32 °C/26 °C) and under standard light regime (16 h photoperiod, 300 µE m2 s−1) or dim light (16 h photoperiod, 25 µE m2 s−1). Seed vigor was assessed during imbibition at 20 °C in the dark in water, 71 mM NaCl or a polyethylene glycol solution (PEG 8000) both corresponding to −0.3 MPa."], ["Description of data collection", "RNA sequencing of total RNA followed by mapping and bioinformatic analysis for differential gene expression and gene set enrichment analyses. Germination data."], ["Data source location", "Institution: Institut de Recherche en Horticulture et Semences, INRA City: Beaucouzé Country: France"], ["Data accessibility", "Repository name: NCBI GEO Data identification number: GSE158641 Direct URL to data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158641https://data.mendeley.com/datasets/6h44fvz8×9/1"]], "row_count": 9, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}, {"id": "asset:table:pmid:33409343:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1cf9a70fcd781ec6cf08521a39872ce2a462273203072c759be42f361411e0d6", "bytes": 1000, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Vigor characteristics of seeds extracted from fruits that ripened ex planta at different temperature and light conditions. After drying, seeds were imbibed in the dark at 20 °C in water, 71 mM Nacl or a PEG 8000 solution corresponding to −0.3 MPa. Data are the mean of three replicates of 50 seeds. Values in brackets represent standard deviation. DL = dim light; HL, high light; HT, high temperature; ST, standard temperature, t50, time of imbibition necessary to reach 50% germination).", "structure": {"pmcid": "PMC7773857", "section_index": 3, "section_title": "Data Description", "row_count": 5, "column_count": 5}, "table": {"label": "Table 1", "caption": "Vigor characteristics of seeds extracted from fruits that ripened ex planta at different temperature and light conditions. After drying, seeds were imbibed in the dark at 20 °C in water, 71 mM Nacl or a PEG 8000 solution corresponding to −0.3 MPa. Data are the mean of three replicates of 50 seeds. Values in brackets represent standard deviation. DL = dim light; HL, high light; HT, high temperature; ST, standard temperature, t50, time of imbibition necessary to reach 50% germination).", "rows": [["Vigor trait", "ST_HL", "ST_DL", "HT_HL", "HT_DL"], ["Germination H2O", "98.0 (2.0)", "86.0 (2.0)", "78.7 (3.1)", "86.0 (4.0)"], ["Speed of germination (t50, d)", "2.8 (0.1)", "3.7 (0.1)", "3.0 (0.1)", "2.7 (0.2)"], ["Germination −0.3 MPa", "31.3 (8.1)", "6.7 (4.2)", "1.3 (1.2)", "3.3 (2.3)"], ["Germination 71 mM NaCl", "23.3 (7.0)", "16.0 (2.0)", "14.0 (5.3)", "12.0 (5.3)"]], "row_count": 5, "column_count": 5, "numeric_cells": 19, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl0001"}}, {"id": "asset:table:pmid:33409343:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8f84e18a1ae3a4185f847215511fdaa5a9feafff92b03a5c30ca122bcc0a77de", "bytes": 1781, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#tbl0002", "version": null, "note": "Summary of mapping information performed with SALMON and FastQC. End, endosperm; Em, embryo, DL = dim light; HL, high light; HT, high temperature; ST, standard temperature.", "structure": {"pmcid": "PMC7773857", "section_index": 3, "section_title": "Data Description", "row_count": 27, "column_count": 6}, "table": {"label": "Table 2", "caption": "Summary of mapping information performed with SALMON and FastQC. End, endosperm; Em, embryo, DL = dim light; HL, high light; HT, high temperature; ST, standard temperature.", "rows": [["Sample Name", "% Aligned", "M Aligned", "% Dups", "% GC", "M Seqs"], ["HT_DL_Em_1", "82.00%", "20.7", "64.60%", "42%", "25.2"], ["HT_DL_Em_2", "83.60%", "20.9", "51.10%", "43%", "25.0"], ["HT_DL_Em_3", "84.80%", "21.5", "61.90%", "43%", "25.3"], ["HT_DL_Em_4", "83.60%", "21.1", "65.40%", "43%", "25.2"], ["HT_DL_End_1", "82.70%", "20.7", "64.60%", "42%", "25.0"], ["HT_DL_End_2", "82.30%", "20.8", "62.80%", "42%", "25.3"], ["HT_DL_End_3", "83.10%", "21.0", "62.60%", "42%", "25.3"], ["HT_HL_Em_1", "81.60%", "20.5", "62.30%", "42%", "25.2"], ["HT_HL_Em_2", "81.60%", "20.7", "60.50%", "42%", "25.4"], ["HT_HL_Em_3", "80.80%", "20.4", "62.80%", "42%", "25.2"], ["HT_HL_End_1", "82.90%", "21.1", "63.60%", "42%", "25.4"], ["HT_HL_End_2", "83.40%", "21.0", "64.00%", "42%", "25.2"], ["HT_HL_End_3", "82.50%", "20.9", "64.40%", "43%", "25.4"], ["ST_DL_Em_1", "83.40%", "20.8", "57.10%", "43%", "24.9"], ["ST_DL_Em_2", "82.70%", "20.8", "59.70%", "42%", "25.2"], ["ST_DL_Em_3", "83.30%", "20.8", "66.90%", "42%", "24.9"], ["ST_DL_End_1", "82.10%", "20.7", "64.40%", "42%", "25.3"], ["ST_DL_End_2", "82.70%", "21.0", "64.50%", "42%", "25.4"], ["ST_DL_End_3", "82.60%", "21.0", "64.50%", "42%", "25.4"], ["ST_HL_Em_1", "81.90%", "20.6", "53.20%", "42%", "25.1"], ["ST_HL_Em_2", "83.30%", "21.1", "60.70%", "42%", "25.4"], ["ST_HL_Em_3", "83.20%", "20.8", "51.70%", "43%", "25.0"], ["ST_HL_Em_4", "82.10%", "20.8", "62.80%", "42%", "25.3"], ["ST_HL_End_1", "82.30%", "20.8", "62.60%", "42%", "25.3"], ["ST_HL_End_2", "83.40%", "21.1", "63.20%", "42%", "25.3"], ["ST_HL_End_3", "82.60%", "20.9", "61.70%", "42%", "25.3"]], "row_count": 27, "column_count": 6, "numeric_cells": 156, "header_rows": 1, "locator": "section[3]/table-wrap[2]#tbl0002"}}, {"id": "asset:table:pmid:33409343:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:24a0657a904cec24478b37a7696994bfb556efb646e80e3cf8ccf4a9bc14e8ec", "bytes": 719, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[3]#tbl0003", "version": null, "note": "Number of differentially expressed genes (DEGs) in embryo and endosperm tissues in different light/temperature conditions compared to standard conditions. Number of DEGs were identified using the DEseq2 algorithm with a Benjamini-Hochberg p-value adjustment threshold set at 0.05 to control false positive rate. DL = dim light; HL, high light; HT, high temperature; ST, standard temperature.", "structure": {"pmcid": "PMC7773857", "section_index": 3, "section_title": "Data Description", "row_count": 5, "column_count": 5}, "table": {"label": "Table 3", "caption": "Number of differentially expressed genes (DEGs) in embryo and endosperm tissues in different light/temperature conditions compared to standard conditions. Number of DEGs were identified using the DEseq2 algorithm with a Benjamini-Hochberg p-value adjustment threshold set at 0.05 to control false positive rate. 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