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team at Kennedy Space Center for their work to validate, prepare and harvest the BRIC LED experiment. 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The experiment concluded with flooding the PDFUs with RNAlater.","name":"growth protocol","parameters":[{"@id":"#139957956687184","parameterName":{"@id":"48YCEaV0OYe5IfhyTjW9adJ0YRPHGeGVZ7fkwAtV","annotationValue":"Mean Growth Temperature","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}},{"@id":"#139957956688864","parameterName":{"@id":"2SqVxiann4K3pa0ERciKn3d2ykBkKCFqbU0aPnTH","annotationValue":"Light Intensity","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}},{"@id":"#139957942942832","parameterName":{"@id":"uRXa2oN701DjkFUq0vnYXDk8xa4w6ppyZhPDjkhG","annotationValue":"growth environment","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0000997","termSource":"OBI"}},{"@id":"#139957942941440","parameterName":{"@id":"WDU9sFcTIi128UsgVfkYd6h6fr21otOMY1ueClNx","annotationValue":"Growth Time","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}},{"@id":"#139957942943552","parameterName":{"@id":"MkIkzYM1jrvWuePq22Rpmhqnp37YDc7MbPDP87wg","annotationValue":"Growth Medium","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":""}},{"@id":"#139957942941536","parameterName":{"@id":"U5WLmwukTxXWgKomF4AHANxTU6mTqcyuanyikHZc","annotationValue":"Quantity of growth medium","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}},{"@id":"#139957942942208","parameterName":{"@id":"Ji6it6B8b3je9ZT1GdWUzB93SpH83aDvgfb4l7R7","annotationValue":"light cycle","comments":[],"termAccession":"http://purl.obolibrary.org/obo/NCIT_C90419","termSource":""}},{"@id":"#139957942943024","parameterName":{"@id":"Tghb7xVngJ45HvCCDliHIprpyUezINnqb21RnQKL","annotationValue":"Light Color","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}}],"protocolType":{"@id":"0gMEkcMNeDUnXJOXyMiO3HWs7cSThiG9RpoYliDD","annotationValue":"growth protocol","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0003789","termSource":"EFO"},"uri":"","version":""},{"@id":"#139957928333216","comments":[],"components":[],"description":"Actuation of the PDFUs, released about 6-7ml RNAlater into the petri plates for seedling fixation on-orbit. The seedlings were then incubated in Invitrogen RNAlater for 12 hours after which they were frozen aboard the ISS at -80 C till returned to Earth. A similar experimental setup was established on the ground at the Kennedy Space Center in Florida in the Space Station Environmental Simulator (ISSES) chamber, USA.  Frozen plates containing both the spaceflight and ground samples were packed in dry ice and transported to Ohio University where they were stored at -80 C prior to protein extraction and processing while another group was also sent to the University of Florida, Gainesville for RNA extraction, library preparation and sequencing.","name":"sample collection","parameters":[{"@id":"#139957942941152","parameterName":{"@id":"eUm691aR7an5kII9bYi7JOSQEcghOzzbVfEjAtOG","annotationValue":"Sample Preservation Method","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139957942942784","parameterName":{"@id":"f35LRInkOhIipZJMj3QqwZfzknHysHZYIWTPkIq5","annotationValue":"Sample Storage Temperature","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}},{"@id":"#139957942943600","parameterName":{"@id":"sP54JsBy5BgphXNcvo5mPkAqnKOiqR4KGLk76HDG","annotationValue":"Age at sample harvest","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}}],"protocolType":{"@id":"9AKy01Zo5kzawArYiQYhNN82sV5bfwRsBjaGG7pr","annotationValue":"sample collection","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139957928330096","comments":[],"components":[],"description":"Seedlings from spaceflight and ground controls were divided into root and shoot for soluble and membrane protein extractions according to a protocol adapted from (Basu et al., 2015). Approximately 0.1g of tissue per replicate was crushed in liquid nitrogen and vortexed thoroughly in the extraction buffer. The samples were subsequently centrifuged at 8000g and 100,000g to isolate membrane protein. Both the precipitated soluble protein stored in methanol and the membrane protein in microsome resuspension buffer were sent to the Proteomics and Metabolomics Facility, at the University of Nebraska, Lincoln for 6-plex TMT labeling and mass spectrometric analysis.","name":"Extraction","parameters":[{"@id":"#139957942942544","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"ONkmhURrVGWoeCtURY6ScDxnfWh5l4BN6fIaG7bV","annotationValue":"Extraction","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139957928329712","comments":[],"components":[],"description":"Briefly, protein samples were assayed using the CB-X protein assay from G-Bioscience. 100ug membrane and 200ug soluble samples in triplicates were reduced and trypsin digested.100ug of each was labeled with 0.8mg each of a unique 6-plexTandem Mass Tag (TMT). Labeled samples were combined into 4 6-plex experiments and 300ug of each was sub-fractioned into 96 fractions using high pH reverse phase C18 chromatography (ACQUITY UPLC BEH C18, 1.7um, 2.1 x 100mm, Waters Corp), and recombined according to the concatenated strategy of Yang et al. to give 6 total fractions. Each of the 6 fractions was analyzed by LC-MS/MS on an RSLCnano system (ThermoFisher Scientific) coupled to an Eclipse Orbitrap Tribrid mass spectrometer (ThermoFisher Scientific).","name":"Labeling","parameters":[{"@id":"#139957942940480","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"dEeweVLu5TkPmeRPDVDa1siyWNv0rpeYtdHTvFii","annotationValue":"Labeling","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139957942941872","comments":[],"components":[],"description":"Following trapping of the peptides (Acclaim PepMap 100, 75um x 2 cm, ThermoFisher Scientific), separation was performed on a C18 nano column (Acquity UPLC M-class, Peptide CSH 130A, 1.7um 75um x 250mm, Waters Corp) at 300 nL/min with a linear gradient from 4-22% over 2 h for a total 2.5h run time.  Peptide  MS2 spectra were acquired using the ion trap with CID activation.  Synchronous Precursor Selection (SPS) using 10 notches was used for the acquisition of MS3 spectra to give the optimal quantification of reporter ion ratios. To minimize the collection of lengthy MS3 spectra, MS2 spectra underwent real-time searching against the canonical version of the Uniprot reference proteome of A. thaliana (downloaded on 17th Feb 2022) during spectral acquisition, with identification triggering MS3 acquisition.  High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS Pro interface) was used to sub-fractionate peptide fractions using 3 compensation voltages (CVs of \u201340, -55 and -70) for deeper coverage. Both FAIMS and SPS help alleviate the negative influence of interfering ions and the ratio compression issues associated with TMT labeling.","name":"Mass Spectrometry","parameters":[{"@id":"#139957959380272","parameterName":{"@id":"zq2d1Oqjy1mLh8OlEBJDdYbzkkyRsSpU2s49apZs","annotationValue":"Instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957959379744","parameterName":{"@id":"vu3p88w3SDuBGHsqoUA46HuIdP5LnsbMqyYRKPFy","annotationValue":"Chromatography","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957959380896","parameterName":{"@id":"GX2TeSxad4YiAGG1Xn3gBViz3BwHRQCJDD7pasUl","annotationValue":"Ion Source","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957959380752","parameterName":{"@id":"otJm7bRihaqxHd2YPRi5JTz1xaYaj3Sk5H7WhsCj","annotationValue":"Dissociation","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957959379312","parameterName":{"@id":"9GkCgUJ1ytQvUu7d4k5XywDkr4nQIUm2TferUhDH","annotationValue":"Detector","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957959380032","parameterName":{"@id":"NGV3yJApFNtJjKJFPEut7HnsTHdHmf2J20xZmFdZ","annotationValue":"Analyzer","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"S3JieWn5H8FnDi46ijrcsL5meeL8bI8oPdbvhieC","annotationValue":"Mass Spectrometry","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139957942941920","comments":[],"components":[],"description":"Data were analyzed in Proteome Discoverer 2.4 software (ThermoFisher Scientific) using the Sequest HT search engine. 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The pooled sample was used to normalize each TMT experiment based on the same sample. The protein ratios and log2 fold change are calculated from the grouped protein abundances. The significance of differential expression is tested using an ANOVA test which provides a p-value and an adjusted p-value using the Benjamini-Hochberg method for all the calculated ratios. Supplemental files contain excel files. Raw and CSV files are provided in the sample table for simplified analysis.","name":"Proteomics Data Processing and Analysis","parameters":[{"@id":"#139957959378400","parameterName":{"@id":"pHvTzjJCVnUZ0D1oDroNfdS4UFMxgc4YNUQCGQi6","annotationValue":"Peptide File Name","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}},{"@id":"#139957959377824","parameterName":{"@id":"GImmrkYSYh5KOAIoEjydiBN2dFigMfcnz7RfIILu","annotationValue":"Protein File Name","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}}],"protocolType":{"@id":"tz29efW08QVQrSxwabMOk8ygrAkvGGxmm8KMEgCc","annotationValue":"Data Processing","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":"EFO"},"uri":"","version":""},{"@id":"#139957942939760","comments":[],"components":[],"description":"For each condition (Spaceflight and Ground), four individual plants from each replicate were pooled for RNA extraction. Individual plants were first dissected into leaves, hypocotyls, and root tissues under an Olympus dissecting microscope (Olympus, Japan). The intervening hypocotyls were set aside and not processed for downstream analyses. Leaf tissues without their hypocotyl are referred to herein as shoots and are the only ones processed for RNA analysis. RNA extraction was performed using the Qiagen RNeasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer\u2019s guidelines. RNA concentration was assessed using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, USA), and RNA quality was determined on the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA). 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The 12 barcoded libraries were sized on the Bioanalyzer and quantified with the Qubit 2.0 Fluorometer. Finally, these 20 individual libraries were pooled in equimolar concentration.","name":"Library Construction","parameters":[{"@id":"#139957945441152","parameterName":{"@id":"SXpkstgzgf9WOhn8BRUImqf5kbHf1TJ3GjkLiaMg","annotationValue":"Library Selection","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957945439616","parameterName":{"@id":"rlzTK2chbZkUcaCWHWpzFmlVUzKNZ7DXWAzUXMTb","annotationValue":"Library Layout","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957945441584","parameterName":{"@id":"FgvdSWC3uI17LsXvErGgSgUHhsklR2Ok3RnEeJgE","annotationValue":"Stranded","comments":[],"termAccession":"","termSource":""}},{"@id":"#139957945442112","parameterName":{"@id":"gtKoOB4pXqmeWeZUfaA9fbez5HqlqkExIy7Egxfe","annotationValue":"Library Kit","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":"OSD"}}],"protocolType":{"@id":"XwjyzSmjqwin5GREdbnjSVPuFEUzn18nShdNZvvS","annotationValue":"Library Construction","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139957959380704","comments":[],"components":[],"description":"The Illumina NovaSeq 6000 was used to sequence the libraries for 2 x 1501cycles. 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