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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 1.3.1). The raw array data files were loaded into R (version 4.1.3) using limma (version 3.50.3). Raw data quality assurance density, pseudo image, MA, and foreground-background plots were generated using limma (version 3.50.3), and boxplots were generated using ggplot2 (version 3.4.0). The raw intensity data was background corrected and normalized across arrays via the limma (version 3.50.3) quantile method. Normalized data quality assurance density, pseudo image, and MA plots were generated using limma (version 3.50.3), and boxplots were generated using ggplot2 (version 3.4.0). Ensembl gene ID mappings were retrieved for each probe using the Ensembl database ftp server (ensembl.org, release 107). Differential expression analysis was performed in R (version 4.1.3) using limma (version 3.50.3); all groups were compared pairwise for each probe to generate a moderated t-statistic and associated p- and adjusted p-value. Gene annotations were assigned using the custom annotation tables generated in-house as detailed in GL-DPPD-7110 (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable_1.0.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable_1.0.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md</a>), with STRINGdb (version 2.8.4), PANTHER.db (version 1.0.11), and org.Ce.eg.db (version 3.15.0).","name":"GeneLab microarray data processing protocol","parameters":[{"@id":"#139850540299264","parameterName":{"@id":"K118AXUyIEG1ZYS51uguXcjP8ntWEkDmw8vHFKwv","annotationValue":"Raw Intensities Table","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139850455906576","parameterName":{"@id":"RpH2RFEgfhHH505JAZKmbs1qSQxqTEWunuvVxI6T","annotationValue":"Normalized Expression Table","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139850455908016","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":""}],"publicReleaseDate":"31-Aug-2021","publications":[{"authorList":"Higashitani A, Hashizume T, Takiura M, Higashitani N, Teranishi M, Oshima R, Yano S, Kuriyama K, Higashibata A.","comments":[],"doi":"10.1038/s41526-021-00163-7","pubMedID":"34471121","status":{"@id":"LmdAvi3HYaAIgsfwpY1sWHGrDR5sHm3luQJDg1Ay","annotationValue":"published","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796","termSource":"EFO"},"title":"Histone deacetylase HDA-4-mediated epigenetic regulation in space-flown C. elegans."},{"authorList":"Sudevan S, Muto K, Higashitani N, Hashizume T, Higashibata A, Ellwood RA, Deane CS, Rahman M, Vanapalli SA, Etheridge T, Szewczyk NJ, Higashitani A.","comments":[],"doi":"10.1016/j.isci.2022.103762","pubMedID":"35141505","status":{"@id":"LmdAvi3HYaAIgsfwpY1sWHGrDR5sHm3luQJDg1Ay","annotationValue":"published","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001796","termSource":"EFO"},"title":"Loss of physical contact in space alters the dopamine system in C. elegans."}],"studyDesignDescriptors":[{"@id":"h0shfCKjUqWbQbBHH9iZLu4lX5tHwbttyXVJiTw5","annotationValue":"transcription profiling by array","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0002768","termSource":"EFO"}],"submissionDate":"06-May-2021","title":"The effect of microgravity on the epigenetic modification in C. elegans - JAXA EPIGENETICS spaceflight experiment","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":6}},"success":true}