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KFT","a100018termsourceref":"","a100019termaccessionnumber":"","a100020characteristicsstratificationexposure":"3-5","a100021unit":"day","a100022termsourceref":"UO","a100023termaccessionnumber":"http://purl.obolibrary.org/obo/UO_0000033","a100024protocolref":"growth protocol","a100025parametervaluegrowthmedium":"0.5% Phytagel-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg's Vitamin Mixture","a100026termsourceref":"OSD","a100027termaccessionnumber":"https://osdr.nasa.gov/","a100028parametervaluequantityofgrowthmedium":"50","a100029unit":"milliliter","a100030termsourceref":"UO","a100031termaccessionnumber":"http://purl.obolibrary.org/obo/UO_0000098","a100032parametervaluelightcycle":"24 light","a100033unit":"hour","a100034termsourceref":"UO","a100035termaccessionnumber":"http://purl.obolibrary.org/obo/UO_0000032","a100036parametervaluelightintensity":"80","a100037unit":"micromole per square meter per 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Celsius","a100058termsourceref":"UO","a100059termaccessionnumber":"http://purl.obolibrary.org/obo/UO_0000027","a100060parametervalueageatsampleharvest":"10","a100061unit":"day","a100062termsourceref":"UO","a100063termaccessionnumber":"http://purl.obolibrary.org/obo/UO_0000033"}],"table":[{"a100000sourcename":"Roots of fixed ground control seedlings, from flight 1, replicate 1","a100001samplename":"GSM4848948","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/NCBITAXON/3702\" title=\"thale-cress\" source=\"NCBITAXON\">Arabidopsis thaliana </a>","a100005characteristicsstrain":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"EFO\">Wassilewskija ecotype </a>","a100008characteristicsgenotype":"pCaMV35S:14-3-3k:GFP ","a100011characteristicsorganismpart":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018517\" title=\"The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990) Bulbs, Plant\" source=\"MESH\">Plant Roots </a>","a100014factorvaluealteredgravity":"Ground control ","a100017factorvaluetime":"Ground Control ","a100020characteristicsstratificationexposure":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">3-5 day</a>","a100024protocolref":"growth protocol","a100025parametervaluegrowthmedium":"0.5% Phytagel-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg's Vitamin Mixture ","a100028parametervaluequantityofgrowthmedium":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000098\" title=\"&quot;A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.&quot; [NIST:NIST] ml, millilitre\" source=\"UO\">50 milliliter</a>","a100032parametervaluelightcycle":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000032\" title=\"&quot;A time unit which is equal to 3600 seconds or 60 minutes.&quot; [Wikipedia:Wikipedia] h\" source=\"UO\">24 light hour</a>","a100036parametervaluelightintensity":"80 micromole per square meter per second","a100040parametervaluelightsource":"fluorescent lighting ","a100043parametervaluelightregimen":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/EO_0007162\" title=\"The treatment involving continuous exposure of light to the plant.\" source=\"EFO\">continuous light regimen </a>","a100046parametervaluemeangrowthtemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">19 degree Celsius</a>","a100050parametervaluehardware":"UF growth room","a100051protocolref":"treatment protocol","a100052protocolref":"sample collection","a100053parametervaluesamplepreservationmethod":"RNALater ","a100056parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100060parametervalueageatsampleharvest":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">10 day</a>"},{"a100000sourcename":"Roots of fixed ground control seedlings, from flight 1, replicate 2","a100001samplename":"GSM4848949","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/NCBITAXON/3702\" title=\"thale-cress\" source=\"NCBITAXON\">Arabidopsis thaliana </a>","a100005characteristicsstrain":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"EFO\">Wassilewskija ecotype </a>","a100008characteristicsgenotype":"pCaMV35S:14-3-3k:GFP ","a100011characteristicsorganismpart":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018517\" title=\"The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990) Bulbs, Plant\" source=\"MESH\">Plant Roots </a>","a100014factorvaluealteredgravity":"Ground control ","a100017factorvaluetime":"Ground Control ","a100020characteristicsstratificationexposure":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">3-5 day</a>","a100024protocolref":"growth protocol","a100025parametervaluegrowthmedium":"0.5% Phytagel-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg's Vitamin Mixture ","a100028parametervaluequantityofgrowthmedium":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000098\" title=\"&quot;A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.&quot; [NIST:NIST] ml, millilitre\" source=\"UO\">50 milliliter</a>","a100032parametervaluelightcycle":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000032\" title=\"&quot;A time unit which is equal to 3600 seconds or 60 minutes.&quot; [Wikipedia:Wikipedia] h\" source=\"UO\">24 light hour</a>","a100036parametervaluelightintensity":"80 micromole per square meter per second","a100040parametervaluelightsource":"fluorescent lighting ","a100043parametervaluelightregimen":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/EO_0007162\" title=\"The treatment involving continuous exposure of light to the plant.\" source=\"EFO\">continuous light regimen </a>","a100046parametervaluemeangrowthtemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">19 degree Celsius</a>","a100050parametervaluehardware":"UF growth room","a100051protocolref":"treatment protocol","a100052protocolref":"sample collection","a100053parametervaluesamplepreservationmethod":"RNALater ","a100056parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100060parametervalueageatsampleharvest":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">10 day</a>"},{"a100000sourcename":"Roots of fixed ground control seedlings, from flight 1, replicate 3","a100001samplename":"GSM4848950","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/NCBITAXON/3702\" title=\"thale-cress\" source=\"NCBITAXON\">Arabidopsis thaliana </a>","a100005characteristicsstrain":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"EFO\">Wassilewskija ecotype </a>","a100008characteristicsgenotype":"pCaMV35S:14-3-3k:GFP ","a100011characteristicsorganismpart":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018517\" title=\"The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990) Bulbs, Plant\" source=\"MESH\">Plant Roots </a>","a100014factorvaluealteredgravity":"Ground control ","a100017factorvaluetime":"Ground Control ","a100020characteristicsstratificationexposure":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">3-5 day</a>","a100024protocolref":"growth protocol","a100025parametervaluegrowthmedium":"0.5% Phytagel-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg's Vitamin Mixture ","a100028parametervaluequantityofgrowthmedium":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000098\" title=\"&quot;A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.&quot; [NIST:NIST] ml, millilitre\" source=\"UO\">50 milliliter</a>","a100032parametervaluelightcycle":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000032\" title=\"&quot;A time unit which is equal to 3600 seconds or 60 minutes.&quot; [Wikipedia:Wikipedia] h\" source=\"UO\">24 light hour</a>","a100036parametervaluelightintensity":"80 micromole per square meter per second","a100040parametervaluelightsource":"fluorescent lighting ","a100043parametervaluelightregimen":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/EO_0007162\" title=\"The treatment involving continuous exposure of light to the plant.\" source=\"EFO\">continuous light regimen </a>","a100046parametervaluemeangrowthtemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">19 degree Celsius</a>","a100050parametervaluehardware":"UF growth room","a100051protocolref":"treatment protocol","a100052protocolref":"sample collection","a100053parametervaluesamplepreservationmethod":"RNALater ","a100056parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100060parametervalueageatsampleharvest":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">10 day</a>"},{"a100000sourcename":"Roots of seedlings fixed in first-actuated KFT, from flight 1, replicate 1","a100001samplename":"GSM4848951","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/NCBITAXON/3702\" title=\"thale-cress\" source=\"NCBITAXON\">Arabidopsis thaliana </a>","a100005characteristicsstrain":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"EFO\">Wassilewskija ecotype </a>","a100008characteristicsgenotype":"pCaMV35S:14-3-3k:GFP ","a100011characteristicsorganismpart":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018517\" title=\"The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990) Bulbs, Plant\" source=\"MESH\">Plant Roots </a>","a100014factorvaluealteredgravity":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018470\" title=\"A change in, or manipulation of, gravitational force. This may be a natural or artificial effect. Gravity, Artificial\" source=\"MESH\">Gravity, Altered </a>","a100017factorvaluetime":"first-actuated KFT ","a100020characteristicsstratificationexposure":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">3-5 day</a>","a100024protocolref":"growth protocol","a100025parametervaluegrowthmedium":"0.5% Phytagel-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg's Vitamin Mixture ","a100028parametervaluequantityofgrowthmedium":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000098\" title=\"&quot;A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.&quot; [NIST:NIST] ml, millilitre\" source=\"UO\">50 milliliter</a>","a100032parametervaluelightcycle":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000032\" title=\"&quot;A time unit which is equal to 3600 seconds or 60 minutes.&quot; [Wikipedia:Wikipedia] h\" source=\"UO\">24 light hour</a>","a100036parametervaluelightintensity":"80 micromole per square meter per second","a100040parametervaluelightsource":"fluorescent lighting ","a100043parametervaluelightregimen":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/EO_0007162\" title=\"The treatment involving continuous exposure of light to the plant.\" source=\"EFO\">continuous light regimen </a>","a100046parametervaluemeangrowthtemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">19 degree Celsius</a>","a100050parametervaluehardware":"UF growth room","a100051protocolref":"treatment protocol","a100052protocolref":"sample collection","a100053parametervaluesamplepreservationmethod":"RNALater ","a100056parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100060parametervalueageatsampleharvest":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">10 day</a>"},{"a100000sourcename":"Roots of seedlings fixed in first-actuated KFT, from flight 1, replicate 2","a100001samplename":"GSM4848952","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/NCBITAXON/3702\" title=\"thale-cress\" source=\"NCBITAXON\">Arabidopsis thaliana </a>","a100005characteristicsstrain":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"EFO\">Wassilewskija ecotype </a>","a100008characteristicsgenotype":"pCaMV35S:14-3-3k:GFP ","a100011characteristicsorganismpart":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018517\" title=\"The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990) Bulbs, Plant\" source=\"MESH\">Plant Roots </a>","a100014factorvaluealteredgravity":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018470\" title=\"A change in, or manipulation of, gravitational force. This may be a natural or artificial effect. Gravity, Artificial\" source=\"MESH\">Gravity, Altered </a>","a100017factorvaluetime":"first-actuated KFT ","a100020characteristicsstratificationexposure":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">3-5 day</a>","a100024protocolref":"growth protocol","a100025parametervaluegrowthmedium":"0.5% Phytagel-based growth medium supplemented with: 0.5x Murashige-Skoog salts, 0.5% (w/v) sucrose, and 1x Gamborg's Vitamin Mixture ","a100028parametervaluequantityofgrowthmedium":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000098\" title=\"&quot;A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.&quot; [NIST:NIST] ml, millilitre\" source=\"UO\">50 milliliter</a>","a100032parametervaluelightcycle":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000032\" title=\"&quot;A time unit which is equal to 3600 seconds or 60 minutes.&quot; [Wikipedia:Wikipedia] h\" source=\"UO\">24 light hour</a>","a100036parametervaluelightintensity":"80 micromole per square meter per second","a100040parametervaluelightsource":"fluorescent lighting ","a100043parametervaluelightregimen":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/EO_0007162\" title=\"The treatment involving continuous exposure of light to the plant.\" source=\"EFO\">continuous light regimen </a>","a100046parametervaluemeangrowthtemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">19 degree Celsius</a>","a100050parametervaluehardware":"UF growth room","a100051protocolref":"treatment protocol","a100052protocolref":"sample collection","a100053parametervaluesamplepreservationmethod":"RNALater ","a100056parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100060parametervalueageatsampleharvest":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000033\" title=\"&quot;A time unit which is equal to 24 hours.&quot; [Wikipedia:Wikipedia]\" source=\"UO\">10 day</a>"},{"a100000sourcename":"Roots of seedlings fixed in first-actuated KFT, from flight 1, replicate 3","a100001samplename":"GSM4848953","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/NCBITAXON/3702\" title=\"thale-cress\" source=\"NCBITAXON\">Arabidopsis thaliana </a>","a100005characteristicsstrain":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"EFO\">Wassilewskija ecotype </a>","a100008characteristicsgenotype":"pCaMV35S:14-3-3k:GFP ","a100011characteristicsorganismpart":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018517\" title=\"The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990) Bulbs, Plant\" source=\"MESH\">Plant Roots </a>","a100014factorvaluealteredgravity":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D018470\" title=\"A change in, or manipulation of, gravitational force. This may be a natural or artificial effect. 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Despite the differing genotypes, experimental workflows, flight profiles and platforms, alteration of gene expression remodeling central metabolic processes was commonly observed as a response to the flights. The processes included carbon and nitrogen metabolism, branched-chain amino acid degradation, and hypoxic responses. The timing and directionality of differentially-expressed genes involved in the conserved pathways differed among the platforms. 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Sense strand DNA was fragmented, biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (ThermoFisher Scientific, Catalog   900670) per the manufacturer's protocol.","name":"Labeling","parameters":[{"@id":"#139924668081824","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"dEeweVLu5TkPmeRPDVDa1siyWNv0rpeYtdHTvFii","annotationValue":"Labeling","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139924668081296","comments":[],"components":[],"description":"3.5 ug of sense DNA was hybridized, with rotation, onto an Affymetrix GeneChip Arabidopsis Gene 1.0 ST Array for 16 h at 45 C. Arrays were washed on a Fluidics Station 450 (ThermoFisher Scientific, Catalog 00-0079) using the Hybridization Wash and Stain Kit (Thermofisher Scientific, Catalog   900720) and the Washing Procedure FS450_0002.","name":"Nucleic Acid Hybridization","parameters":[{"@id":"#139924668081920","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"Ds5U52KXWGMCUj85Xzb7xXlQahYabetbZxYQOx7G","annotationValue":"Nucleic Acid Hybridization","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139924668082640","comments":[],"components":[],"description":"Total RNA was extracted from roots comprising each replicate and submitted for microarray analysis. The Affymetrix GeneChip Arabidopsis Gene (AraGene) 1.0 ST array was used to measure gene expression levels. The transcriptomic data from the flight-actuated samples were then compared to those of the ground controls in order to identify differentially-expressed genes between the ground control and the two flight conditions.","name":"Data Collection","parameters":[{"@id":"#139924668082976","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"aDEizhRz0daWSB2Gps2fM88el5h72edi83NoKkwU","annotationValue":"Data Collection","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#139924668083840","comments":[],"components":[],"description":"Data were processed as described in GL-DPPD-7114 (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Affymetrix/Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Affymetrix/Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md</a>) using NF_MAAffymetrix version 1.0.1 (GitHub link coming soon).  In short, a RunSheet containing raw data file location and processing metadata from the study's *ISA.zip file was generated using dp_tools (version 1.3.2). The raw array data files were loaded into R (version 4.1.3) using oligo (version 1.58.0). Raw data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version 1.58.0). The raw probe level intensity data was background corrected and normalized across arrays via the oligo (version 1.58.0) quantile method. Normalized probe level data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version 1.58.0).  Normalized probe level data was summarized to the probeset level using the oligo (version 1.58.0) RMA method. Ensembl gene ID mappings were retrieved for each probeset using the Plants Ensembl database ftp server (plants.ensembl.org, release 54). Differential expression analysis was performed in R (version 4.1.3) using limma (version 3.50.3); all groups were compared pairwise for each probeset to generate a moderated t-statistic and associated p- and adjusted p-value. 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