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The wrapped plates were stored at temperatures between 4 and 10C until launch within a cold stowage bag nominally at 4C. The seeds remained dormant until removed from cold storage and exposed to light at the initiation of the experiment on the ISS (International Space Station). Plant growth on the ISS and ISSES (International Space Station Environment Simulator): The APEX03-2 experiment plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS. The 10-cm2 Petri plates were housed perpendicular (vertical) to the overhead LED lighting of the VPS. Plants received between 100-135umoles/m2/s PAR inside the VPS. Four and eight days after germination was initiated by unwrapping the plates and exposing them to light in the VPS. The ground control plates were grown inside the VPS ground unit within the ISSES (ISS Environmental Simulator) chamber at KSC with the 48-h delay. The ISSES chamber replicated the temperature, CO2 levels and lighting that had been experienced by the spaceflight plants in the previous 48h.","name":"growth protocol","parameters":[{"@id":"#139989845669632","parameterName":{"@id":"3eJ4QJs154TXdIdLiDlu5RGIZSFgVuhZDvPNF5eR","annotationValue":"light source","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0400065","termSource":"OBI"}},{"@id":"#139989845671264","parameterName":{"@id":"tLgc96Y9UbuifM8yz6aBimTKesyBkF9xeucWIHxJ","annotationValue":"Hardware","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845667952","parameterName":{"@id":"o8F0v46nMoT3hQQDUkcwfLctE2nGYWFMRPsV5kiX","annotationValue":"Growth time","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845671552","parameterName":{"@id":"uRXa2oN701DjkFUq0vnYXDk8xa4w6ppyZhPDjkhG","annotationValue":"growth environment","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0000997","termSource":"OBI"}},{"@id":"#139989845668048","parameterName":{"@id":"MkIkzYM1jrvWuePq22Rpmhqnp37YDc7MbPDP87wg","annotationValue":"Growth Medium","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":""}},{"@id":"#139989845668672","parameterName":{"@id":"CVtRqj2K89Aj185x5f4MNtoo4FxtpQaSB3alMf2T","annotationValue":"Mean Growth Temperature","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845668624","parameterName":{"@id":"tCOWJ65rGKGI8DtdvTKGilFfvkzWu2jH3PRS8yl4","annotationValue":"Light quality","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845668240","parameterName":{"@id":"Ji6it6B8b3je9ZT1GdWUzB93SpH83aDvgfb4l7R7","annotationValue":"light cycle","comments":[],"termAccession":"http://purl.obolibrary.org/obo/NCIT_C90419","termSource":""}},{"@id":"#139989845671120","parameterName":{"@id":"LP7iGRskWBD8hbvmdsPfLgMlMCmrYyLoXJU4NNI7","annotationValue":"Light intensity","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"0gMEkcMNeDUnXJOXyMiO3HWs7cSThiG9RpoYliDD","annotationValue":"growth protocol","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0003789","termSource":"EFO"},"uri":"","version":""},{"@id":"#139989854122912","comments":[],"components":[],"description":"On Orbit Operations and harvest: At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI freezer. Following Dragon Capsule splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80C freezer. The PIs retrieved the plant samples from the KFTs and transferred the samples back to the University of Florida. The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment. Seedlings stored in RNAlater were recovered from -80C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. Roots of the preserved seedlings from the spaceflight and ground control harvests were dissected and the rest of the seedlings were saved in RNAlater and stored back to -80C freezer. For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.","name":"sample collection","parameters":[{"@id":"#139989843025296","parameterName":{"@id":"eUm691aR7an5kII9bYi7JOSQEcghOzzbVfEjAtOG","annotationValue":"Sample Preservation Method","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989843022272","parameterName":{"@id":"vbrzINCaNhslTc1WulmcigpF6afqM7x3H1PCAdm0","annotationValue":"Sample Storage Temperature","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}}],"protocolType":{"@id":"9AKy01Zo5kzawArYiQYhNN82sV5bfwRsBjaGG7pr","annotationValue":"sample collection","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139989843025728","comments":[],"components":[],"description":"Total RNA was extracted using Qiashredder and RNAeasy kits from QIAGEN (QIAGEN Sciences, MD, USA) according to the manufacturer's instructions. Residual DNA was removed by performing an on-column digestion using an RNase Free DNase (QIAGEN GmbH, Hilden, Germany). Integrity of the RNA was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).","name":"Nucleic Acid Extraction","parameters":[{"@id":"#139989843025488","parameterName":{"@id":"Hop5C9AJDN9g3VYqtIJtB2A611oQjKFpzG6shAoZ","annotationValue":"QA Instrument","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"SUvQ2YF4kYqggIqs6nZbO3jPYZOOa6kg99LuQwua","annotationValue":"Nucleic Acid Extraction","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139989843022944","comments":[],"components":[],"description":"Ten ng of total RNA was used for cDNA library construction using CloneTech SMART-Seq V4 ultra low input RNA kit for sequencing (Clontech Laboratories, Inc, cat : 634890) according to manufacturer's protocol. Briefly, 1st strand cDNA was primed by the SMART-Seq v4 oligonucleotide and then base-pairs with these additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting full-length cDNA that contains an anchor sequence that serves as a universal priming site for second strand synthesis. cDNA was amplified with primer II A for 8 PCR cycles. Then Illumina sequencing libraries were generated with 150 pg of cDNA using Illumina Nextera DNA Sample Preparation Kit (Cat : FC-131-1024) according to manufacturer's instructions. Briefly, 150 pg of cDNA was fragmented by tagementation reaction and then adapter sequences added onto template cDNA by PCR amplification. Libraries were quantitated by Bioanalyzer and qPCR (Kapa Biosystems, catalog number: KK4824). Finally, the libraries were pooled equal molar concentration and sequenced by Illumina 2X76 NextSeq 500.","name":"Library Construction","parameters":[{"@id":"#139989832834736","parameterName":{"@id":"SXpkstgzgf9WOhn8BRUImqf5kbHf1TJ3GjkLiaMg","annotationValue":"Library Selection","comments":[],"termAccession":"","termSource":""}},{"@id":"#139989832833728","parameterName":{"@id":"rlzTK2chbZkUcaCWHWpzFmlVUzKNZ7DXWAzUXMTb","annotationValue":"Library Layout","comments":[],"termAccession":"","termSource":""}},{"@id":"#139989832834256","parameterName":{"@id":"FgvdSWC3uI17LsXvErGgSgUHhsklR2Ok3RnEeJgE","annotationValue":"Stranded","comments":[],"termAccession":"","termSource":""}},{"@id":"#139989832833584","parameterName":{"@id":"8WYoCyz2C7EHCUeJopWqPTSkwz6WD98uPi77l4Ik","annotationValue":"Library Kit","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"XwjyzSmjqwin5GREdbnjSVPuFEUzn18nShdNZvvS","annotationValue":"Library Construction","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139989843023424","comments":[],"components":[],"description":"Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida. In preparation for sequencing, barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems, catalog number: KK4824). Individual samples were pooled equimolarly at 4 nM. This working pool was used as input in the NextSeq500 instrument sample preparation protocol (Illumina, Part   15048776, Rev A). Typically, a 1.3 pM library concentration resulted in optimum clustering density in our instrument (i.e., ~200,000 clusters per mm2). Samples were sequenced on 5 flowcells (5 NextSeq 500 runs), using a 2x76 cycles (paired-end) configuration. A typical sequencing run in the NextSeq500 produced 750-800 million paired-end read with a Q30 greater or equal to 85%. For RNA seq, around 40 million reads provided sufficient depth for transcriptome analysis.","name":"Nucleic Acid Sequencing","parameters":[{"@id":"#139989832832528","parameterName":{"@id":"QZv3O6FfjrX7Rj1AdVBpE7MMkvX0gDPFNyhTgsul","annotationValue":"Sequencing Instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#139989832832864","parameterName":{"@id":"bN7ocR6S7OMQu0NaaGuljRlHf2Wjd9p6RkRYRYxX","annotationValue":"Read Length","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":""}}],"protocolType":{"@id":"PsdoouSqq1TS1MOsEV6KSaZ1z6HqOAcEOC3cEEVX","annotationValue":"Nucleic Acid Sequencing","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139989843024048","comments":[],"components":[],"description":"Merged raw reads files were generated using sratools (version 2.11.0) to fetch associated SRA files for each sample and extract raw reads and finally concatenate into forward and reverse raw reads files. Raw fastq files from each sample were assessed for % rRNA using HTStream SeqScreener (version 1.3.2) screened against a fasta file of Arabidopsis thaliana rRNA sequences retrieved from NCBI on 01-Sep-2021. Raw fastq file quality was evaluated with FastQC (version 0.12.1) and MultiQC (version 1.26) was used to generate MultiQC reports.","name":"GeneLab\u00a0raw data processing protocol","parameters":[{"@id":"#139989832834112","parameterName":{"@id":"AETaHseEwkszM2rFw5vBNeaU6DHhetrpZYXxWDUi","annotationValue":"Read Depth","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":""}},{"@id":"#139989832833488","parameterName":{"@id":"RaWNd099ZqS9NO9TqfvpU9arANv1Do2iAJueQJMm","annotationValue":"rRNA Contamination","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989832832240","parameterName":{"@id":"XGdRyLdFBrQ5sINQ7N8WhowWQEznWY4WnzAmBL6l","annotationValue":"Merged Sequence Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989856707680","parameterName":{"@id":"WoqQnOe0wYp5oJdMtNlLbe7bcXgG6P1BgtOCncYd","annotationValue":"MultiQC File Names","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""},{"@id":"#139989832833248","comments":[],"components":[],"description":"Data were processed as described in GL-DPPD-7101-G (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/blob/master/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/blob/master/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md</a>), using NF_RCP version 2.1.0 (https://github.com/nasa/GeneLab_RNASeq_Workflow/tree/NF_RCP_2.1.0). In short, raw fastq files were filtered using Trim Galore! (version 0.6.10) powered by Cutadapt (version 4.2). Trimmed fastq file quality was evaluated with FastQC (version 0.12.1), and MultiQC (version 1.26) was used to generate MultiQC reports. Arabidopsis Thaliana STAR and RSEM references were built using STAR (version 2.7.11b) and RSEM (version 1.3.3), respectively, Ensembl Plants release 59, genome assembly TAIR10 (Arabidopsis_thaliana.TAIR10.dna.toplevel.fa) and the following gtf annotation file: Arabidopsis_thaliana.TAIR10.59.gtf. Trimmed reads were aligned to the Arabidopsis Thaliana STAR reference with STAR (version 2.7.11b) and alignment log files were compiled with MultiQC (version 1.26). Aligned reads were assessed for strandedness using RSeQC infer_experiment.py (version 5.0.4), gene body coverage using RSeQC geneBody_coverage.py (version 5.0.4), inner distance was assessed using RSeQC inner_distance.py (version 5.0.4), and distribution of RNA features using RSeQC read_distribution.py (version 5.0.4). Aligned reads from all samples were quantified using RSEM (version 1.3.3), with strandedness set to none and RSEM count log files were compiled with MultiQC (version 1.26). To create a set of rRNA-removed quantification data, Ensembl IDs mapping to ribosomal RNA (rRNA) were removed from the RSEM gene count data. Both the original set of RSEM quantification data and the rRNA-removed data were subject to differential gene expression analysis as follows. A runsheet was generated with dp_tools (version 1.3.8) and the runsheet and quantification data were imported to R (version 4.4.2) with tximport (version 1.34.0) and normalized with DESeq2 (version 1.46.0) median of ratios method. Normalized gene counts were subject to differential expression analysis. Differential expression analysis was performed in R (version 4.4.2) using DESeq2 (version 1.46.0); all groups were compared pairwise using the Wald test and the likelihood ratio test was used to generate the F statistic p-value. 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.At.tair.db (version 3.19.1).","name":"GeneLab RNAseq data processing protocol","parameters":[{"@id":"#139989837616272","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002569","termSource":"OBI"}},{"@id":"#139989845668912","parameterName":{"@id":"ppE5corBvOu9AEyW9bYn5gFyngDSKhDRof0PnkDl","annotationValue":"Trimmed Sequence Data/Multiqc Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845671072","parameterName":{"@id":"s2HskUjUzSQmahcRYDfv1xBVjYScvewE8EO773hd","annotationValue":"Trimmed Sequence Data/Trimming Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845671408","parameterName":{"@id":"lqpWRJZ7O2rPhdA4uPNANCqeFig4cQhw07RfB2f5","annotationValue":"aligned sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002580","termSource":"OBI"}},{"@id":"#139989845669584","parameterName":{"@id":"3AwnKZQDUPRaMntinM9bvBrGHpnb8qc6GaaZRIQh","annotationValue":"Aligned Sequence Data/Alignment Logs","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845668096","parameterName":{"@id":"ib7AEGeVUoAruCpz91Qn6GXdO3E5d8k0DSeT2EQR","annotationValue":"Aligned Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845670448","parameterName":{"@id":"QcbiokEiY9OO2PO8IXfNhCwNUeMq4JM2ugyguLO3","annotationValue":"RSeQC/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845669488","parameterName":{"@id":"CzV3xNixKDCRnULWE97WbT9v456v77sgf4dPZG0Y","annotationValue":"Raw Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845669680","parameterName":{"@id":"sNs9cWTm8FSfHsQQiZSOB2rREx6z4B3etvs29HfB","annotationValue":"Raw Counts Data/Multiqc Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845671168","parameterName":{"@id":"WXhsQG8JLZ5oK8kUYbPxGSfXi520yz8A4dEHcBKs","annotationValue":"Raw Counts Tables","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845668768","parameterName":{"@id":"Lns3jxVPjBQ2dUuFO7KyPzSqST1hCHcuYbzwld4i","annotationValue":"Normalized Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989845671600","parameterName":{"@id":"c4UoiNar4sA4ty0VawH08rhaf4AR7F8drWBP91tt","annotationValue":"differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"OBI"}},{"@id":"#139989845669056","parameterName":{"@id":"SPhWEr1D3r2VJ9OKO5b94MEY02Ipod6UwkLtQaRk","annotationValue":"Aligned Sequence Data/Unmapped Reads","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""}],"publicReleaseDate":"24-Feb-2018","publications":[],"studyDesignDescriptors":[{"@id":"bY0pyszHil7hCZtviw2VrENWVTKYDHZ2OJlQDQon","annotationValue":"low earth orbit","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00000019","termSource":"RBO"}],"submissionDate":"24-Feb-2017","title":"Plant development on ISS differs from the development on the ground and is influenced by the genetic background","unitCategories":[{"@id":"0egjOe4tupLenTJ2RAdBhRffOpl8xZWv0FRLbF9W","annotationValue":"day","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000033","termSource":""},{"@id":"ixhZXi79C7bGPbpBgn0nhYS3WcKUHFxvfrXat1ju","annotationValue":"degree Celsius","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000027","termSource":""},{"@id":"3NsFnd66zdjAOh2GC6fP6tV74K8EwvLJtvhxvA9L","annotationValue":"micromole per square meter per second","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000160","termSource":""}]}],"version":10}},"success":true}