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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. SG2 was sent to the International Space Station (ISS) during the SpaceX CRS-4 (September 2014) and returned on CRS-5 (February 2015), and SG3 was sent to the ISS during the SpaceX CRS-11 campaign (June 2017) and returned a month later, on the same mission. Details of ISS dosimetry and a table with doses for all GeneLab ISS experiment ISS datasets are available at <a href=\"https://genelab.nasa.gov/environmental/radiation.\" target=\"_\" >https://genelab.nasa.gov/environmental/radiation.</a>  Seeds were dormant at launch, then germinated and grown for six days, then harvested and frozen. 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RNA Integrity Number were above 7.","name":"nucleic acid extraction","parameters":[{"@id":"#139989935035056","parameterName":{"@id":"Hop5C9AJDN9g3VYqtIJtB2A611oQjKFpzG6shAoZ","annotationValue":"QA Instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#139989955643424","parameterName":{"@id":"AKFULPaZzL2J22DNBTdtRb681TVpFMeJj3ziEprY","annotationValue":"QA Assay","comments":[],"termAccession":"","termSource":""}},{"@id":"#139989955642032","parameterName":{"@id":"HzDLlLTGaZjIbBNDIQmjCNLDXJ93jptTzCf2uo5X","annotationValue":"QA Score","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"wMWjvygtA0CrXbq6WiPP8h2TZP3fdPfCR1KVuno7","annotationValue":"nucleic acid extraction","comments":[],"termAccession":"","termSource":"OBI"},"uri":"","version":""},{"@id":"#139989938847504","comments":[],"components":[],"description":"Seventeen total RNA samples (representing six experimental conditions with three biological replicates each except one of the spaceflight experiment sample) were used to generate seventeen sequencing libraries using the Illumina TruSeq RNA Library Preparation Kit (Illumina, USA). 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Aligned reads from all samples were quantified using RSEM (version 1.3.3), with strandedness set to reverse 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":"#139989957360464","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002569","termSource":"OBI"}},{"@id":"#139989957357872","parameterName":{"@id":"S1Mj22Y7OVW5vzLBnk1GH1BlSpGG85V4ZqDGty94","annotationValue":"Trimmed Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957358928","parameterName":{"@id":"WpCrX7ide25WusZiM5fIrSKdZyPYtYpeIuZuH3Sl","annotationValue":"Trimmed Sequence Data/Trimming Reports","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957358640","parameterName":{"@id":"lqpWRJZ7O2rPhdA4uPNANCqeFig4cQhw07RfB2f5","annotationValue":"aligned sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002580","termSource":"OBI"}},{"@id":"#139989957357824","parameterName":{"@id":"d79SF6NoEsF121WRmPPzZiwVwNLu3Z61vAbDb3DP","annotationValue":"Aligned Sequence Data/Alignment Logs","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957359456","parameterName":{"@id":"g250OL2tOApNgqHpsOhSdEc7YPv37WMxqzczbWan","annotationValue":"Aligned Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957359648","parameterName":{"@id":"u5CcOVGJQ0XaquJnrbuSFIagziBYwOsfUr3dkbSF","annotationValue":"RSeQC/MultiQC Reports","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957358448","parameterName":{"@id":"VtCeJt5tCH5Mou8N5WaS6rsW7vVjUCBVpB1fudZ2","annotationValue":"Raw Counts Data","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957358784","parameterName":{"@id":"ITmhLA2FjuufSjH1QJL5jhkTXuWe9RXydYXY1bXo","annotationValue":"Raw Counts Data/MultiQC Reports","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957358976","parameterName":{"@id":"qE26QFh1gGK9QpA3VnntTzcq3gFfnMhwzwovbTnn","annotationValue":"Raw Counts Tables","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957358592","parameterName":{"@id":"OpDtY8r5bfPp9J80gwSysYM09RYYDmTPzfUt7y87","annotationValue":"Normalized Counts Data","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139989957359216","parameterName":{"@id":"SPhWEr1D3r2VJ9OKO5b94MEY02Ipod6UwkLtQaRk","annotationValue":"Aligned Sequence Data/Unmapped Reads","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139989957359264","parameterName":{"@id":"xKb1sgGDZn43IN8RpDvyhZ9nhWMlHOCwfAS6uXAu","annotationValue":"differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"EFO"}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""}],"publicReleaseDate":"20-Jan-2021","publications":[{"authorList":"Villacampa A, Ciska M, Manzano A, Vandebrink JP, Kiss JZ, Herranz R and Medina FJ","comments":[],"doi":"10.3390/ijms22020899","pubMedID":"","status":{"@id":"LmdAvi3HYaAIgsfwpY1sWHGrDR5sHm3luQJDg1Ay","annotationValue":"published","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796","termSource":"EFO"},"title":"From Spaceflight to Mars g-Levels: Adaptive Response of A. Thaliana Seedlings in a Reduced Gravity Environment Is Enhanced by Red-Light Photostimulation"}],"studyDesignDescriptors":[{"@id":"4RixOBC6fhf4nbWNsIBIHQNECE6Cps7f9LJdaqgK","annotationValue":"transcription profiling by high throughput sequencing","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0002770","termSource":"EFO"},{"@id":"ye61g042HicvNesXww8Tqg6eQYoqkVSNreZPKs9O","annotationValue":"space station","comments":[],"termAccession":"http://purl.obolibrary.org/obo/RBO_00000046","termSource":"RBO"}],"submissionDate":"13-Jan-2021","title":"Adaptive response of Arabidopsis seedlings in microgravity and Mars reduced gravity environment is enhanced by red light photostimulation","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":"q4aPyorfWUSzovzJYVk5YmBA3TwiGacDeU8pjYsA","annotationValue":"hour","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000032","termSource":"UO"},{"@id":"K246gUcR0J8GQugx16wEPg241n60ivvdhS6reQoa","annotationValue":"micromole per square meter per second","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}]}],"version":7}},"success":true}