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Vetted batches of seeds were planted on Phytagel plates. One genotype was planted per plate, and six plates were planted of each genotype. One complete set of 18 plates was planted for growth on the International Space Station (ISS), and a comparable set of 18 plates was planted 24 hours later for the ground controls. The plates were wrapped such that every surface of the plate was covered by at least two layers of Duvetyne Black-Out cloth (Seattle Fabrics) to help preserve dormancy. The plates were stored at 4C until launch (six days). The plates of the CARA experiment launched on April 18th, 2014 in a cold-stow bag to maintain the plates at 4C within the Dragon Capsule. The dormant plates were activated on the ISS by bringing them out of cold stowage and removing the Black-Out cloth wrapping, 12 days after launch. The plants were allowed to grow on orbit for 13 days; some in the ambient light of ISS and some in the dark. A standard light meter was not available on the ISS, so ambient light levels were approximated through the use of iPad (iPad3, iOS 5.1.1) application 'Light Meter HD- lux measurement tool', which was executed by astronaut Steve Swanson. Light Treatment Group: It was estimated that the light-grown plates received between 4-6 micromoles per square meter per second of total light. Dark Treatment Group: The dark-grown plates were first activated by exposure to light, (the Black-Out cloth was removed from the designated plates for 4 hours), and then re-wrapped in Black-Out cloth for the duration of the growth period.","name":"growth protocol","parameters":[{"@id":"#139783003814304","parameterName":{"@id":"3eJ4QJs154TXdIdLiDlu5RGIZSFgVuhZDvPNF5eR","annotationValue":"light source","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0400065","termSource":"OBI"}},{"@id":"#139783003813536","parameterName":{"@id":"tLgc96Y9UbuifM8yz6aBimTKesyBkF9xeucWIHxJ","annotationValue":"Hardware","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139783003812672","parameterName":{"@id":"uRXa2oN701DjkFUq0vnYXDk8xa4w6ppyZhPDjkhG","annotationValue":"growth environment","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0000997","termSource":"OBI"}},{"@id":"#139783003815456","parameterName":{"@id":"Bzz7bu7517gUzkIRMUJTkNUM69gax5CL2S2nGCNa","annotationValue":"Growth Time","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":"#139782950166336","comments":[],"components":[],"description":"At 13 days, most seedlings were photographed, and then harvested into Kennedy Space Center Fixation Tubes (KFTs) containing RNAlater. The plants were allowed to perfuse for 12\u201318 hours at ambient temperature within the KFTs, and then the KFTs were transferred to the MELFI (Minus Eighty-degree Laboratory Freezer for ISS). The frozen KFTs were returned to cold stowage within the Dragon Capsule at the end of the docked operations period, and were returned to Earth on May 18, 2014. Following the Dragon Capsule splashdown in the Pacific Ocean, the frozen KFTs were 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 on May 22, 2014. The PIs retrieved the plant samples from the KFTs on May 29, 2014 and transferred the frozen samples back to the University of Florida. A comparable set of plates and operations comprised the experimental control set (referred to as the ground control). The plates of the ground control were grown at Kennedy Space Center (KSC) within the ISS Environment Simulator (ISSES) Chamber. The ground control was initiated 24 hours after the initiation of the spaceflight experiment to facilitate the programing the ISSES Chamber with the ISS environmental conditions experienced by the flight plates in the prior 24 hours. The environmental parameters that were monitored and then programed into the ISSES chamber included temperature, CO2 and relative humidity. In addition, the lighting in the ISSES chamber was adjusted to recapitulate the light levels being experienced by the plants on orbit. Light measurements in the ISSES chamber were taken with the same iPad model and operating system (iPad3, iOS 5.1.1) used on the ISS, with the 'Light Meter HD- lux measurement tool' application.","name":"sample collection","parameters":[{"@id":"#139782950163168","parameterName":{"@id":"eUm691aR7an5kII9bYi7JOSQEcghOzzbVfEjAtOG","annotationValue":"Sample Preservation Method","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139782950165904","parameterName":{"@id":"vbrzINCaNhslTc1WulmcigpF6afqM7x3H1PCAdm0","annotationValue":"Sample Storage Temperature","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}}],"protocolType":{"@id":"zaKRMPLXOBudyE1ROMNBjnZXViwkiB6PT7wea0yd","annotationValue":"sample collection","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#139782950163120","comments":[],"components":[],"description":"Seedlings stored in RNA later were recovered from -80C freezer. 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Total RNA was extracted from these frozen samples using Picopure RNA isolation kit (Arcturus, Life technologies). RNA concentration was determined on a Qubit (Thermo Fisher/Life Technologies, Inc) and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). Five ng RNA from each sample was used for low input array and RNA sequencing.","name":"Nucleic Acid Extraction","parameters":[{"@id":"#139783004225600","parameterName":{"@id":"Hop5C9AJDN9g3VYqtIJtB2A611oQjKFpzG6shAoZ","annotationValue":"QA Instrument","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"hvmnimkOSUuDnRXoMCmOVO622eV9H3rhB5Orz2Zc","annotationValue":"Nucleic Acid Extraction","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#139782950164368","comments":[],"components":[],"description":"RNASeq Libraries Preparation using SMART-Seq V4 ultra low input RNA kit for sequencing combined with Illumina Nextera DNA Sample Preparation Kit. 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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":"#139783003815840","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002569","termSource":"OBI"}},{"@id":"#139783003812864","parameterName":{"@id":"s2HskUjUzSQmahcRYDfv1xBVjYScvewE8EO773hd","annotationValue":"Trimmed Sequence Data/Trimming Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139783003813056","parameterName":{"@id":"Paz4Pjo6sV6E66RG3a9xuZDjKKpk7ywwq3VwmAwn","annotationValue":"Trimmed Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139783003812480","parameterName":{"@id":"lqpWRJZ7O2rPhdA4uPNANCqeFig4cQhw07RfB2f5","annotationValue":"aligned sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002580","termSource":"OBI"}},{"@id":"#139783003814160","parameterName":{"@id":"SPhWEr1D3r2VJ9OKO5b94MEY02Ipod6UwkLtQaRk","annotationValue":"Aligned Sequence Data/Unmapped Reads","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139783003812384","parameterName":{"@id":"3AwnKZQDUPRaMntinM9bvBrGHpnb8qc6GaaZRIQh","annotationValue":"Aligned Sequence Data/Alignment Logs","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139783003813680","parameterName":{"@id":"ib7AEGeVUoAruCpz91Qn6GXdO3E5d8k0DSeT2EQR","annotationValue":"Aligned Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139783003815744","parameterName":{"@id":"QcbiokEiY9OO2PO8IXfNhCwNUeMq4JM2ugyguLO3","annotationValue":"RSeQC/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973110256","parameterName":{"@id":"CzV3xNixKDCRnULWE97WbT9v456v77sgf4dPZG0Y","annotationValue":"Raw Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973109728","parameterName":{"@id":"WXhsQG8JLZ5oK8kUYbPxGSfXi520yz8A4dEHcBKs","annotationValue":"Raw Counts Tables","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973110448","parameterName":{"@id":"w31o7Q91WYOVYIwRCqOCvdUs4H84WG2M5y8Qgu1N","annotationValue":"Raw Counts Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973111216","parameterName":{"@id":"Lns3jxVPjBQ2dUuFO7KyPzSqST1hCHcuYbzwld4i","annotationValue":"Normalized Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973112128","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":"#139783004228864","comments":[],"components":[],"description":"The developmental progress of plant growth was followed through a series of photographs taken by the attending astronaut on the ISS, and by the attending technician at KSC, providing an independent 'pseudonaut' on the ground in order to mimic astronaut activities on the ISS. The photographs in figure 2 of the article show representative images that compared the progress of growth after 3d, 6d and 9d for each genotype. The photographs were often taken through the back of each plate. The region of interest was cropped from each astronaut-captured photograph to better display the progress of plant development. The photography taken on the ISS used Nikon cameras, whereas the ground control used a Panasonic camera. OSDR staff extracted parameter 'Plate Number' from the raw image files and reported here.","name":"Image Analysis","parameters":[{"@id":"#139782973110880","parameterName":{"@id":"Tg93UAsK6RU8nyicrSoyZjwUoXeIYJEZrdJsFHjT","annotationValue":"Camera Make And Model","comments":[],"termAccession":"","termSource":""}},{"@id":"#139782973110832","parameterName":{"@id":"5ZQGXTYmnpv6UXlGYlCQE2i0PHsMwUORebeCPuUE","annotationValue":"Exposure Mode","comments":[],"termAccession":"","termSource":""}},{"@id":"#139782973111456","parameterName":{"@id":"0d0G1NEDmSPfmWYcgWbxeqPqrPwrFIjUM6v3jZpH","annotationValue":"Aperture Of Photo Or F Stop","comments":[],"termAccession":"","termSource":""}},{"@id":"#139782973111744","parameterName":{"@id":"lB2vjpLqIuSQAE9YeearxfNHfPQDhIP5GuAvJMuQ","annotationValue":"Focal Length Of Photo","comments":[],"termAccession":"","termSource":""}},{"@id":"#139782973109344","parameterName":{"@id":"c9Ig7v2b7pSIaJ1mYiB0lKvRsfOvf2DSievs2fEL","annotationValue":"Color Space Or Channels","comments":[],"termAccession":"","termSource":""}},{"@id":"#139782973111024","parameterName":{"@id":"YdgrhF23qXGn4MZzWUTFgFc5ery7J4fMrvRUqkYM","annotationValue":"exposure time","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973109200","parameterName":{"@id":"W9Uf8zGC2ILqLF9YUChD1gca24k62duGHUTYHPQb","annotationValue":"Date Photo Taken YYYY-MM-DD","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973108576","parameterName":{"@id":"EgaJIDWev4lLiH8tDc0QU16RSxEwVyVGtXH3vRHg","annotationValue":"Raw image files","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973111360","parameterName":{"@id":"DGV9hMSMQW4UIMO9VZaN45PHezg1PrcvYf4jTTvn","annotationValue":"Image Dimensions Height Y","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139782973110400","parameterName":{"@id":"uNkDVXcOhLXhUb9iA7wXx2sAG883msAkOoTUrvm6","annotationValue":"Image Dimensions Width X","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"iW8DB9W9GC1DO9EniCKx0abRjWp9Z3jJrobzU16A","annotationValue":"Image Analysis","comments":[],"termAccession":"","termSource":""},"uri":"","version":""}],"publicReleaseDate":"08-Jun-2017","publications":[{"authorList":"Paul AL, Sng NJ, Zupanska AK, Krishnamurthy A, Schultz ER, Ferl RJ.","comments":[],"doi":"10.1371/journal.pone.0180186","pubMedID":"28662188","status":{"@id":"cfwAwavSGugL54m5pQGCxkplxzpfut4vvBkXLzDG","annotationValue":"Published","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796","termSource":""},"title":"Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight?"}],"studyDesignDescriptors":[{"@id":"G18x8YsiHNJtkVdmhg9hAuzPv2Xvir8TpCqjEpRS","annotationValue":"low Earth orbit","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00000019","termSource":"RBO"}],"submissionDate":"02-Jun-2017","title":"Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight?","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":""}]}],"version":14}},"success":true}
