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We also very much appreciate the on orbit support of the experiment by astronaut crew. We thank the Interdisciplinary Centre for Biological Research (ICBR, University of Florida) team, particularly Yanping Zhang, Alberto Riva and William Farmerie for the gene expression and bioinformatics services they provided. We would also like to thank the members of the UF space plants laboratory, particularly Jordan Callaham, for their general support."},{"name":"DOI","value":"10.26030/j07k-nm86"},{"name":"Data Source Accession","value":"GSE95620"},{"name":"Data Source Link","value":"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE95620"},{"name":"Experiment Platform","value":"Vegetable Production System (VPS/Veggie)"},{"name":"Flight Program","value":"Internation Space Station (ISS)"},{"name":"Funding","value":"The work was supported by grant number GA-2013-104, Center for Advancement of Science in Space (CASIS), URL: http://www.iss-casis.org/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."},{"name":"Identifiers","value":""},{"name":"Managing NASA Center","value":"Kennedy Space Center (KSC)"},{"name":"Mission End","value":"02/11/2015"},{"name":"Mission Link","value":"https://osdr.nasa.gov/bio/repo/data/missions/SpaceX-5"},{"name":"Mission Name","value":"SpaceX-5"},{"name":"Mission Start","value":"01/10/2015"},{"name":"Project Identifier","value":"APEX-03-2"},{"name":"Project Link","value":""},{"name":"Project Title","value":""},{"name":"Project Type","value":"Spaceflight study"},{"name":"Space Program","value":"NASA"},{"name":"Study Grant Number","value":"GA-2013-104"}],"description":"The wild type WS plants and the Sku5 mutant plants in the WS background were germinated on ISS or on the ground and the gene expression profiles in roots at 4 days or 8 days were established. The Sku5 gene (AT4G12420) codes for a multi-copper oxidase-like protein SKU5 protein that is involved in directed root tip growth. The Sku5 protein is glycosylated, GPI-anchored and localizes to the plasma membrane and the cell wall. The Sku5 gene is expressed most strongly in expanding tissues. The development of WS and Sku5 plants on orbit differs from that on the ground as demonstrated by the comparison of the gene expression profiles between 4 days old to 8 days old plant in the two environments. However the development of Sku5 mutant plants also differs from WS at either age and in either environment, suggesting the role of the genetic background in these developmental decisions. The 4 days old Sku5 roots in orbit engaged substantially more genes than the 4 days old WS roots in orbit but also more than the 4 days old Sku5 roots on the ground. Overall the 4 days old roots differentially expressed more genes in spaceflight relative to ground than the 8 days old roots of either genotype. Finally, the 4 days old Sku5 roots in orbit differ in 862 genes from the 8 days Sku5 roots in orbit while on the ground there is merely half of the number of genes differentially expressed between the 4 days and 8 days developmental stages of the Sku5 roots. APEX03-2 (Advanced Plant Experiment 03-2) also identified as TAGES-Isa (Transgenic Arabidopsis Gene Expression System\u2014Intracellular Signaling Architecture) was launched on SpaceX mission CRS-5 on 10 January 2015. Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). 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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":"#139835865549792","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002569","termSource":"OBI"}},{"@id":"#139835865550416","parameterName":{"@id":"ppE5corBvOu9AEyW9bYn5gFyngDSKhDRof0PnkDl","annotationValue":"Trimmed Sequence Data/Multiqc Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865550224","parameterName":{"@id":"s2HskUjUzSQmahcRYDfv1xBVjYScvewE8EO773hd","annotationValue":"Trimmed Sequence Data/Trimming Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865550272","parameterName":{"@id":"lqpWRJZ7O2rPhdA4uPNANCqeFig4cQhw07RfB2f5","annotationValue":"aligned sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002580","termSource":"OBI"}},{"@id":"#139835865549504","parameterName":{"@id":"3AwnKZQDUPRaMntinM9bvBrGHpnb8qc6GaaZRIQh","annotationValue":"Aligned Sequence Data/Alignment Logs","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865549120","parameterName":{"@id":"ib7AEGeVUoAruCpz91Qn6GXdO3E5d8k0DSeT2EQR","annotationValue":"Aligned Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865549264","parameterName":{"@id":"QcbiokEiY9OO2PO8IXfNhCwNUeMq4JM2ugyguLO3","annotationValue":"RSeQC/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865548976","parameterName":{"@id":"CzV3xNixKDCRnULWE97WbT9v456v77sgf4dPZG0Y","annotationValue":"Raw Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865548016","parameterName":{"@id":"sNs9cWTm8FSfHsQQiZSOB2rREx6z4B3etvs29HfB","annotationValue":"Raw Counts Data/Multiqc Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865547920","parameterName":{"@id":"WXhsQG8JLZ5oK8kUYbPxGSfXi520yz8A4dEHcBKs","annotationValue":"Raw Counts Tables","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865548112","parameterName":{"@id":"Lns3jxVPjBQ2dUuFO7KyPzSqST1hCHcuYbzwld4i","annotationValue":"Normalized Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139835865548352","parameterName":{"@id":"c4UoiNar4sA4ty0VawH08rhaf4AR7F8drWBP91tt","annotationValue":"differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"OBI"}},{"@id":"#139835865547488","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":"01-Mar-2020","publications":[{"authorList":"Anna-Lisa Paul, Natasha J. Sng, Agata K. Zupanska, Aparna Krishnamurthy, Eric R. Schultz, Robert J. Ferl","comments":[],"doi":"10.1371/journal.pone.0180186","pubMedID":"28662188","status":{"@id":"LmdAvi3HYaAIgsfwpY1sWHGrDR5sHm3luQJDg1Ay","annotationValue":"published","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796","termSource":"EFO"},"title":"Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight?"}],"studyDesignDescriptors":[{"@id":"4RixOBC6fhf4nbWNsIBIHQNECE6Cps7f9LJdaqgK","annotationValue":"transcription profiling by high throughput sequencing","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0002770","termSource":"EFO"}],"submissionDate":"02-Mar-2017","title":"During development, the Sku5 mutant roots engage different genes than wild type WS roots, either on the ground or in spaceflight.","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":"IyqYoEBAjUnYrSULnflKfFRmLhLMQAE68YRB9lRQ","annotationValue":"\u03bcmoles/m2/s PAR","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}]}],"version":5}},"success":true}