Time-course microarray transcriptome data of in vitro cultured testes and age-matched in vivo testes.

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Here, we provide a dataset of time-course microarray transcriptome data of in vitro cultured neonate murine testes and age-matched in vivo-derived testes. The dataset presented here is related to the article titled \"Transcriptome analysis reveals inadequate spermatogenesis and immediate radical immune reactions during organ culture in vitro spermatogenesis\" published in Biochemical and Biophysical Research Communications in 2020 [1]. The raw data and pre-processed data are publicly available on the GEO repository (accession number GSE147982). Furthermore, the dataset provided here includes additional metadata, detailed explanations of the experiment, results of pre-processing, analysis scripts, and lists of differentially expressed genes from in vitro culture testes and in vivo testes at each time point.", "claims": [{"id": "claim-method", "statement": "Supplementary Table 1 provides the result of differential expression analysis, which is done using an empirical moderated t-statistics test with a cut-off adjusted p-value of 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33241095", "locator": "sections[3] \"Data Description\" paragraph 2", "quote": "Supplementary Table 1 provides the result of differential expression analysis, which is done using an empirical moderated t-statistics test with a cut-off adjusted p-value of 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data and pre-processed data are publicly available on the GEO repository (accession number GSE147982).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33241095", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw data and pre-processed data are publicly available on the GEO repository (accession number GSE147982)."}], "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:33241095"], "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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The in vitro cultured testes are then collected and subjected to total RNA extraction. The total RNA from in vivo-derived testes of corresponding aged mice to the cultured testes were also extracted. The quality of the total RNA was checked and microarray analysis were performed by Illumina MouseWG-6 v2.0 Expression beadchip."], ["Data source location", "RIKEN Center for Integrative Medical Sciences1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan"], ["Data accessibility", "Repository name: Gene Expression OmnibusData identification number: GSE147982Direct URL to data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147982"], ["Related research article", "Takeru Abe, Hajime Nishimura, Takuya Sato, Harukazu Suzuki, Takehiko Ogawa, Takahiro Suzuki, Time-course microarray transcriptome data of in vitro cultured testes and corresponding in vivo testes. Biochem Biophys Res Commun. 530 (2020) 732-738https://doi.org/10.1016/j.bbrc.2020.06.161"]], "row_count": 10, "column_count": 2, "numeric_cells": 6, "header_rows": 0, "locator": "section[1]/table-wrap[1]#utbl0001"}}, {"id": "asset:table:pmid:33241095:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:58e19f3e9dbbc44e2c3ae21278b0d05bff799bf161973b1bd8dcbfc87e1c2bc2", "bytes": 1537, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Origin of RNA sample. The abbreviation “dpp” corresponds days post-partum (days-old) and “cddp” corresponds corresponding days post-partum, which is age-matched sample to the in vivo derived testes. 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