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Trimmed reads were aligned to the Drosophila Melanogaster + ERCC STAR reference with STAR (version 2.7.11b) and alignment log files were compiled with MultiQC (version 1.26). 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 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), ERCC genes were removed, and the non-ERCC genes were normalized with DESeq2 (version 1.46.0) median of ratios method. Normalized gene counts were subject to differential expression analysis. Note that since greater than 60% of the reads in sample KCNQ97 Female Space Flown-24 were classified as unalignable to the transcriptome by RSEM, it was excluded from count normalization and 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.Dm.eg.db (version 3.19.1). Assessment of ERCC spiked genes was performed as detailed in the ERCC_analysis_GLbulkRNAseq.html report.","name":"GeneLab RNAseq data processing protocol","parameters":[{"@id":"#140101569123280","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002569","termSource":"OBI"}},{"@id":"#140101569123856","parameterName":{"@id":"s2HskUjUzSQmahcRYDfv1xBVjYScvewE8EO773hd","annotationValue":"Trimmed Sequence Data/Trimming Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569123520","parameterName":{"@id":"Paz4Pjo6sV6E66RG3a9xuZDjKKpk7ywwq3VwmAwn","annotationValue":"Trimmed Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569124480","parameterName":{"@id":"lqpWRJZ7O2rPhdA4uPNANCqeFig4cQhw07RfB2f5","annotationValue":"aligned sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002580","termSource":"OBI"}},{"@id":"#140101569125776","parameterName":{"@id":"SPhWEr1D3r2VJ9OKO5b94MEY02Ipod6UwkLtQaRk","annotationValue":"Aligned Sequence Data/Unmapped Reads","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569123088","parameterName":{"@id":"3AwnKZQDUPRaMntinM9bvBrGHpnb8qc6GaaZRIQh","annotationValue":"Aligned Sequence Data/Alignment Logs","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569126112","parameterName":{"@id":"ib7AEGeVUoAruCpz91Qn6GXdO3E5d8k0DSeT2EQR","annotationValue":"Aligned Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569125824","parameterName":{"@id":"QcbiokEiY9OO2PO8IXfNhCwNUeMq4JM2ugyguLO3","annotationValue":"RSeQC/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569124432","parameterName":{"@id":"CzV3xNixKDCRnULWE97WbT9v456v77sgf4dPZG0Y","annotationValue":"Raw Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569125680","parameterName":{"@id":"WXhsQG8JLZ5oK8kUYbPxGSfXi520yz8A4dEHcBKs","annotationValue":"Raw Counts Tables","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569123904","parameterName":{"@id":"w31o7Q91WYOVYIwRCqOCvdUs4H84WG2M5y8Qgu1N","annotationValue":"Raw Counts Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569125200","parameterName":{"@id":"Lns3jxVPjBQ2dUuFO7KyPzSqST1hCHcuYbzwld4i","annotationValue":"Normalized Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140101569122512","parameterName":{"@id":"c4UoiNar4sA4ty0VawH08rhaf4AR7F8drWBP91tt","annotationValue":"differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"OBI"}},{"@id":"#140101569122656","parameterName":{"@id":"RU82pDdGEcbsiezMzkaKgjf1MKkk9FaQCjynpZUS","annotationValue":"ERCC Analyses","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"ri5yLDcUdyRB0z4kzA3DpS3BdOAyUjsS3o864Ozb","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"EFO"},"uri":"","version":""},{"@id":"#140101576051680","comments":[],"components":[],"description":"Protein extraction was performed using the Norgen RNA/Protein/DNA Purification Kit (Cat#51600).","name":"protein extraction","parameters":[{"@id":"#140101569124096","parameterName":{"@id":"Hop5C9AJDN9g3VYqtIJtB2A611oQjKFpzG6shAoZ","annotationValue":"QA Instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#140101569122992","parameterName":{"@id":"AKFULPaZzL2J22DNBTdtRb681TVpFMeJj3ziEprY","annotationValue":"QA Assay","comments":[],"termAccession":"","termSource":""}},{"@id":"#140101569125152","parameterName":{"@id":"HzDLlLTGaZjIbBNDIQmjCNLDXJ93jptTzCf2uo5X","annotationValue":"QA Score","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"Ji5yT140p0fnnQmvM4pOJHMphA6zWKfMrilcBaqv","annotationValue":"extraction","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#140102260118624","comments":[],"components":[],"description":"Samples were processed using the Thermo Orbitrap Fusion Lumos. 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