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Scientific Research on Innovative Area from MEXT (18H04989 and 19H04821) (T. 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Gene annotations were assigned using the custom annotation tables generated in-house as detailed in GL-DPPD-7110-A (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable-A_1.1.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A.md\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable-A_1.1.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A.md</a>), with STRINGdb (version 2.16.4), PANTHER.db (version 1.0.12), and org.Mm.eg.db (version 3.19.1).","name":"GeneLab RNAseq data processing protocol","parameters":[{"@id":"#139808228450992","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002569","termSource":"OBI"}},{"@id":"#139808228452432","parameterName":{"@id":"s2HskUjUzSQmahcRYDfv1xBVjYScvewE8EO773hd","annotationValue":"Trimmed Sequence Data/Trimming Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808228453440","parameterName":{"@id":"Paz4Pjo6sV6E66RG3a9xuZDjKKpk7ywwq3VwmAwn","annotationValue":"Trimmed Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808228451040","parameterName":{"@id":"lqpWRJZ7O2rPhdA4uPNANCqeFig4cQhw07RfB2f5","annotationValue":"aligned sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002580","termSource":"OBI"}},{"@id":"#139808228453632","parameterName":{"@id":"SPhWEr1D3r2VJ9OKO5b94MEY02Ipod6UwkLtQaRk","annotationValue":"Aligned Sequence Data/Unmapped Reads","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808228450704","parameterName":{"@id":"3AwnKZQDUPRaMntinM9bvBrGHpnb8qc6GaaZRIQh","annotationValue":"Aligned Sequence Data/Alignment Logs","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808228452720","parameterName":{"@id":"ib7AEGeVUoAruCpz91Qn6GXdO3E5d8k0DSeT2EQR","annotationValue":"Aligned Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808228452144","parameterName":{"@id":"QcbiokEiY9OO2PO8IXfNhCwNUeMq4JM2ugyguLO3","annotationValue":"RSeQC/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808228453344","parameterName":{"@id":"CzV3xNixKDCRnULWE97WbT9v456v77sgf4dPZG0Y","annotationValue":"Raw Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808228452576","parameterName":{"@id":"WXhsQG8JLZ5oK8kUYbPxGSfXi520yz8A4dEHcBKs","annotationValue":"Raw Counts Tables","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808222496224","parameterName":{"@id":"w31o7Q91WYOVYIwRCqOCvdUs4H84WG2M5y8Qgu1N","annotationValue":"Raw Counts Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808222496656","parameterName":{"@id":"Lns3jxVPjBQ2dUuFO7KyPzSqST1hCHcuYbzwld4i","annotationValue":"Normalized Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808222496320","parameterName":{"@id":"c4UoiNar4sA4ty0VawH08rhaf4AR7F8drWBP91tt","annotationValue":"differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"OBI"}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""},{"@id":"#139808228367616","comments":[],"components":[],"description":"Pre-acclimation of mice was conducted in the Space Station Processing Facility Science Annex at Kennedy Space Center (KSC) in Florida, USA. Twelve C57BL/6 J male mice (8-week-old for MHU-1 and 9-week-old for MHU-2) in transportation cage units (TCU) were launched aboard the SpaceX rocket from the KSC and transported to the ISS. On board, mice were transferred to habitat cage units (HCU) and housed singly under AG (1 \u00d7 g on the bottom floor of the HCU, at a centrifugation speed of 77 rpm) or MG environments. In the return process, all mice were transferred to TCUs, and the Dragon vehicle loaded with the TCUs was splashed down in the Pacific Ocean off the coast of California, USA. Returned TCUs were transported to a port in Long Beach by ship, and then to the tissue collection site by road. The ground control experiment replicating the housing conditions of the flight experiment was conducted at the JAXA Tsukuba Space Center in Japan.","name":"Animal Husbandry","parameters":[{"@id":"#139808222496368","parameterName":{"@id":"5LOH95NqO1PibD64Tc6A28QJrnLh2tE7xddrCjtO","annotationValue":"Habitat","comments":[],"termAccession":"","termSource":""}},{"@id":"#139808221736048","parameterName":{"@id":"nwqaTeCTIOWF70qWmmwzljM3dpF6sqCjcprxrhlW","annotationValue":"duration","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0000433","termSource":""}},{"@id":"#139808221735088","parameterName":{"@id":"wnjgyTd8rj1O0Oqecf2wG5bXCMq8VGJ9M4evlXyk","annotationValue":"Feeding Schedule","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139808221735520","parameterName":{"@id":"QraHOmTwDKeoAzQ4qV8YkHG42OwaUEmQEmnFZeeT","annotationValue":"Diet","comments":[],"termAccession":"http://purl.bioontology.org/ontology/MESH/D004032","termSource":"MESH"}}],"protocolType":{"@id":"YR4LNS2eFUFmIFimd2AdS4c5IPFCV6D6wUydL8eN","annotationValue":"Animal Husbandry","comments":[],"termAccession":"","termSource":"OBI"},"uri":"","version":""},{"@id":"#139808229439856","comments":[],"components":[],"description":"Following euthanasia, thymi were removed and cut, and a quarter of the thymi was snap-frozen in OCT compound (Sakura Finetek, Japan) and a second quarter of the thymus was used for RNA preparation. Thymi for RNA preparation was quickly frozen in liquid N2, and kept in dry ice and then in a \u221280 \u00b0C freezer.","name":"sample collection","parameters":[{"@id":"#139808221733744","parameterName":{"@id":"Xv0M9pE0aUSn3kUQ9KB3uLrvghDs8N2ndH4aj4iN","annotationValue":"Sample Preservation Method","comments":[],"termAccession":"","termSource":""}},{"@id":"#139808221734416","parameterName":{"@id":"SfwXET3g26o3EFRmOAglaMjl4Hy74pLFl6SkMJ6U","annotationValue":"Sample Storage Temperature","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"pqZaoqneZ2lZZxPSbQTnG1BJvoLNB5ZezLAN4MCe","annotationValue":"sample collection","comments":[],"termAccession":"","termSource":"OBI"},"uri":"","version":""},{"@id":"#139808229438272","comments":[],"components":[],"description":"The absorbed dose of ionizing radiation received by biological payloads on the International Space Station (ISS) depends on a number of factors, including date and duration of exposure and location of the payload on the ISS. Some of the factors that lead to variations in the absorbed dose rate in orbit are ISS altitude, period during the solar cycle, and location of the sample\u2014the ISS module and the specific location within that module. Shielding effects from the biological payload container or habitat have not been taken into account. The measured absorbed dose can vary based on the dosimetry instrument(s) used. Radiation monitoring on the ISS is not standardized across modules; each international partner has its own suite of instruments, with differing technologies, sensitivities and analysis methodologies, including criteria for distinguishing between lightly ionizing particles (mainly protons) and highly ionizing particles (mainly galactic cosmic ray nuclei). Both active and passive dosimeters are used. Active dosimeters are powered and data are read out and stored and/or telemetered to ground. Some active dosimeters provide additional levels of detail such as time resolution, energy deposition and particle identification. Passive dosimeters are unpowered, record constantly and are read out upon return to the ground. The dose in the metadata is the dose recorded by the radiation detector closest to the sample. In most cases that detector will be in the same ISS module; in cases where data from a detector in the same module are not available, the dose is extrapolated using data from periods where data are available from detectors in multiple modules, including the module containing the payload. The duration of the experiment is defined as the time in space during which the specimen was \u201cliving\u201d, including the time on the delivery vehicle (e.g. SpaceX Dragon). Once the specimen was frozen or fixed, the experiment was considered stopped. Details of ISS dosimetry and a table with doses for all GeneLab ISS experiment ISS datasets are available at <a href=\"https://www.nasa.gov/reference/osdr-environmental-data/.\" target=\"_\" >https://www.nasa.gov/reference/osdr-environmental-data/.</a>","name":"radiation dosimetry","parameters":[{"@id":"#139808229375184","parameterName":{"@id":"lqLio6cqwPLox7b7EOdXHJ7fG5xPrPcfHhTTkQZ8","annotationValue":"ionizing radiation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00000116","termSource":""}},{"@id":"#139808229375328","parameterName":{"@id":"QGnq1ZBQG4r5UwZvMZGasxLy3jjaU9tV0a0umLcR","annotationValue":"absorbed radiation dose","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00005010","termSource":""}},{"@id":"#139808229373504","parameterName":{"@id":"VLcA0Jh7NixB76VQ4OBV7LW1GUZ2UUZuZIXAAKG7","annotationValue":"absorbed radiation dose rate","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00005011","termSource":""}},{"@id":"#139808229375232","parameterName":{"@id":"Lp5EqgE3XmDjGm9zXQ0ycUYqNGhgqk7dAGaBWOL1","annotationValue":"exposure duration","comments":[],"termAccession":"http://purl.obolibrary.org/obo/NCIT_C83280","termSource":"NCIT"}},{"@id":"#139808229372736","parameterName":{"@id":"BddYzuysUrqvYNdykuGz2QCiArMDgZ7aJoUWw5gu","annotationValue":"ionizing radiation categorized by source","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00000001","termSource":""}},{"@id":"#139808229374320","parameterName":{"@id":"wxFiRV5BXWlvDgeF3X09uHa7lhc46XznlQpBu4F5","annotationValue":"vehicle","comments":[],"termAccession":"http://purl.obolibrary.org/obo/ENVO_01000604","termSource":""}}],"protocolType":{"@id":"hi70Jsh2JPHiNZpMPZjxM9aOsMJ0hYELnMwknsmS","annotationValue":"chronic","comments":[],"termAccession":"http://purl.obolibrary.org/obo/PATO_0001863","termSource":"EFO"},"uri":"","version":""}],"publicReleaseDate":"04-Jan-2020","publications":[{"authorList":"Kenta Horie, Tamotsu Kato, Takashi Kudo, Hiroki Sasanuma, Maki Miyauchi, Nobuko Akiyama, Takahisa Miyao, Takao Seki, Tatsuya Ishikawa, Yuki Takakura, Masaki Shirakawa, Dai Shiba, Michito Hamada, Hyojung Jeon, Nobuaki Yoshida, Jun-ichiro inoue, Masafumi Muratani, Satoru takahashi, Hiroshi ohno & Taishin Akiyama","comments":[],"doi":"10.1038/s41598-019-56432-9","pubMedID":"31882694","status":{"@id":"LmdAvi3HYaAIgsfwpY1sWHGrDR5sHm3luQJDg1Ay","annotationValue":"published","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796","termSource":"EFO"},"title":"Impact of spaceflight on the murine thymus and mitigation by exposure to artificial gravity during spaceflight"}],"studyDesignDescriptors":[{"@id":"4RixOBC6fhf4nbWNsIBIHQNECE6Cps7f9LJdaqgK","annotationValue":"transcription profiling by high throughput sequencing","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0002770","termSource":"EFO"}],"submissionDate":"04-Jan-2020","title":"Impact of spaceflight on gene expression in the thymus","unitCategories":[{"@id":"HD9tp2SLnR0wXOGt79HG2Wa7QP9SkYuVwR6aCHGl","annotationValue":"day","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000033","termSource":"UO"},{"@id":"rXEqs7vuV48f7fvwnkTqN785nMDguXNcuEYyqAKs","annotationValue":"degree Celsius","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000027","termSource":"UO"},{"@id":"SHRIFGDc50meal3f60aKnlHyc0mXQoqiyW1BovrZ","annotationValue":"milligray","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000142","termSource":"UO"},{"@id":"kQ7xX41a7tbtWDBfRbxYY3YI0jpDae5GiMFij6BD","annotationValue":"milligray per day","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0010063","termSource":"UO"},{"@id":"EN78WNpG5NZElsP9sj1OVW0TMS8NNuDr1mEzIqd2","annotationValue":"week","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000034","termSource":"UO"}]}],"version":7}},"success":true}