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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. 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Three replicates in each condition (12-15 heads per replicate) were used for protein isolation and enzymatic digestion. Isolated protein samples were digested and desalted according to Lundby et al. (Lundby et al., 2012). Protein concentrations were then determined using a bicinchoninic acid assay (BCA) (Thermo-Fisher Scientific, San Jose, CA). Proteins were then reduced, alkylated and subjected to acetone precipitation prior to digestion with endoproteinase Lys-C, 1:50 enzyme to protein (Wako, Richmond, VA). This was followed by digestion with trypsin, 1:50 enzyme to protein (Promega, Madison, WI), and desalting and concentrating using C18 Sep-Pak cartridges (Waters).","name":"protein extraction","parameters":[{"@id":"#139783110312192","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"oTgwL9HykHsIsl3RkHDXvkGYAABLPIDE7enT2qsQ","annotationValue":"extraction","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0302884","termSource":"OBI"},"uri":"","version":""},{"@id":"#139783138114240","comments":[],"components":[],"description":"Peptides were mass tagged using Thermo-Fisher\u2019s TMT 10-plex isobaric label kit (Catalog   90061) following the included protocol and pooled for analysis. Six experimental conditions were labeled in triplicate across three TMT-runs, including two internal control channels.","name":"Labeling","parameters":[{"@id":"#139783113228832","parameterName":{"@id":"tnCJqE1VrwiWBZ77kigpPWNII3z9UckKz4noRxpK","annotationValue":"Run Number","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}}],"protocolType":{"@id":"Ql08vxcqEiFSaj6ao2h3rTog1eN0D0ftX5DBRD9r","annotationValue":"Labeling","comments":[],"termAccession":"","termSource":"OBI"},"uri":"","version":""},{"@id":"#139783125996304","comments":[],"components":[],"description":"Basic Reversed-Phase Fractionation \u2013 Pooled TMT-labeled peptides were fractionated by basic pH reversed-phase (BPRP) fractionation on an Ultimate 3000 HPLC (Thermo Scientific) using an integrated fraction collector. Elution was performed using a 10-minute gradient of 0-20% solvent B followed by a 50-minute gradient of solvent B from 20-45% (Solvent A 5.0% Acetonitrile, 10mM ammonium bicarbonate pH 8.0, Solvent B 90.0% Acetonitrile, 10mM ammonium bicarbonate pH 8.0) on a Zorbax 300Extend-C18 column (Agilent) at a flow rate of 0.4 ml/min. A total of 24 fractions were collected at 37-second intervals in a looping fashion for 60 minutes then combined to produce 12 super fractions. Peptide elution was monitored at a wavelength of 220nm using a Dionex Ultimate 3000 variable wavelength detector (Thermo Scientific). Each fraction was then centrifuged to near dryness and desalted using C18 Sep-Pak Cartridges followed again by centrifugation to near dryness and reconstitution with 20 ul of 5% acetonitrile and 0.1% formic acid.\n\nLiquid Chromatography and Mass Spectrometry- BPRP fractions were then separated using an UltiMate 3000 RSLCnano system (Thermo Scientific, San Jose, CA) on a self-packed C18 column (100 um x 35 cm). Separation was performed using a 180-minute gradient of solvent B from 2-27% (Solvent A 0.1% Formic Acid, Solvent B Acetonitrile, 0.1% Formic Acid) at 50\u00baC using a digital PicoView nanospray source (New Objectives, Woburn, MA) that was modified with a custom-built column heater and an ABIRD background suppressor (ESI Source Solutions, Woburn, MA). An in-house column was prepared by packing a 100\u03bcm inner diameter picofrit column (New Objectives, Woburn, MA) with 1.9\u03bcm ReproSil-Pure C18 (Dr. Maisch, Ammerbuch, Germany) and packed to a length of 30 cm at 9000 psi using a nano-LC column packing kit (nanoLCMS, Gold River, CA). Mass spectral analysis was performed using an Orbitrap Fusion mass spectrometer (Thermo Scientific, San Jose, CA). TMT analysis was performed using an MS3 multi-notch approach. The MS1 precursor selection range is from 400-1400 m/z at a resolution of 120K and automatic gain control (AGC) target of 2.0 x 10^5 with a maximum injection time of 100 ms. Quadrupole isolation at 0.7 Th for MS2 analysis using CID fragmentation in the linear ion trap with a collision energy of 35%. The AGC was set to 4.0 x 10^3 with a maximum injection time of 150ms.  The instrument was operated in a top-speed data-dependent mode with a most intense precursor priority with dynamic exclusion set to an exclusion duration of 60 seconds with a 10ppm tolerance. MS2 fragment ions were captured in the MS3 precursor population. These MS3 precursors were then isolated within a 2.5 Da window and subjected to high energy collision-induced dissociation (HCD) with a collision energy of 55%. The ions were then detected in the Orbitrap at a resolution of 60,000 with an AGC of 5.0 x 10^4 and a maximum injection time of 150 ms. The data was then analyzed using SEQUEST (Thermo Fisher Scientific, San Jose, CA, version v.27, rev. 11.) and Proteome Discoverer (Thermo Scientific, San Jose, CA. version 2.1).","name":"Mass Spectrometry","parameters":[{"@id":"#139783095684688","parameterName":{"@id":"zq2d1Oqjy1mLh8OlEBJDdYbzkkyRsSpU2s49apZs","annotationValue":"Instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#139783095682816","parameterName":{"@id":"vu3p88w3SDuBGHsqoUA46HuIdP5LnsbMqyYRKPFy","annotationValue":"Chromatography","comments":[],"termAccession":"","termSource":""}},{"@id":"#139783095684112","parameterName":{"@id":"GX2TeSxad4YiAGG1Xn3gBViz3BwHRQCJDD7pasUl","annotationValue":"Ion Source","comments":[],"termAccession":"","termSource":""}},{"@id":"#139783095683344","parameterName":{"@id":"otJm7bRihaqxHd2YPRi5JTz1xaYaj3Sk5H7WhsCj","annotationValue":"Dissociation","comments":[],"termAccession":"","termSource":""}},{"@id":"#139783095682144","parameterName":{"@id":"9GkCgUJ1ytQvUu7d4k5XywDkr4nQIUm2TferUhDH","annotationValue":"Detector","comments":[],"termAccession":"","termSource":""}},{"@id":"#139783095683872","parameterName":{"@id":"NGV3yJApFNtJjKJFPEut7HnsTHdHmf2J20xZmFdZ","annotationValue":"Analyzer","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"fnrcVNIyvNzXxQZtjf3ahTCHuSl4WUFUabTwVlI1","annotationValue":"Mass Spectrometry","comments":[],"termAccession":"","termSource":"OBI"},"uri":"","version":""},{"@id":"#139783110315552","comments":[],"components":[],"description":"Tandem mass spectra were extracted, and charge states were deconvoluted by Proteome Discoverer version 2.1. Assignment of MS/MS spectra was performed using SequestHT (Thermo Fisher Scientific, San Jose, CA, USA) by searching the data against a protein database, including all entries from the Uniprot Drosophila proteome (UniProt UP00000803, containing 21,041 sequences, download date 10-29-2019) combined with the common contaminants sequences from the Global Proteome Machine. Sequest searches were performed using a parent ion tolerance of 1.25 Da, fragment ion mass tolerance of 1.00005 Da, and requiring each peptides\u2019 termini to have trypsin protease specificity while allowing up to two missed cleavages. Carbamidomethylation of cysteine residues (+57.02146 Da) was set as static modification, while TMT tags on peptide N termini/lysine residues (+229.162932 Da), acetylation of the protein N-terminus, and methionine oxidation (+15.99492 Da) was set as variable modification. Reporter Ions Quantifier settings were set to include unique and razor peptides, Quan value correction factors from manufacturer applied, co-isolation threshold 50%, average reporter S/N 10, and no normalization or scaling of the channels.","name":"Data Transformation","parameters":[{"@id":"#139783095683968","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""}],"publicReleaseDate":"08-Sep-2022","publications":[{"authorList":"Mhatre Siddhita D., Iyer Janani, Petereit Juli, Dolling-Boreham Roberta M., Tyryshkina Anastasia, Paul Amber M., Gilbert Rachel, Jensen Matthew, Woolsey Rebekah J., Anand Sulekha, Sowa Marianne B., Quilici David R., Costes Sylvain V., Girirajan Santhosh, Bhattacharya Sharmila","comments":[],"doi":"10.1016/j.celrep.2022.111279","pubMedID":"36070701","status":{"@id":"KCcgWp3UEIavjeSzie263Dprx0jUIW7U2H1xTblp","annotationValue":"submitted","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001794","termSource":"EFO"},"title":"Artificial gravity partially protects space-induced neurological deficits in Drosophila melanogaster"}],"studyDesignDescriptors":[{"@id":"PDmY1sKTXFdQ1hZVG6o5TrZ6BxH0kq1JMb1RuJZC","annotationValue":"Gravity, Altered","comments":[],"termAccession":"http://purl.bioontology.org/ontology/MESH/D018470","termSource":"MESH"},{"@id":"XJ2x9G5FYOhyGGbYDO0xkevuzcPxPnzdf1nFa9fv","annotationValue":"Space Flight","comments":[],"termAccession":"http://purl.bioontology.org/ontology/MESH/D013026","termSource":"MESH"},{"@id":"0eJ0zKNMVofUfGOeHImjRFNfS7FcqIdlXd9ikRfD","annotationValue":"growth condition design","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0001759","termSource":"EFO"},{"@id":"ugZYURVS0P0aj0mu2nsC1l4rFTDwH81Uw7YF89kw","annotationValue":"Drosophila","comments":[],"termAccession":"http://purl.bioontology.org/ontology/MESH/D004330","termSource":"MESH"}],"submissionDate":"21-Jun-2022","title":"Artificial gravity partially protects space-induced neurological deficits in Drosophila melanogaster","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":""},{"@id":"s4mQc0cEaxmkRxH4swt1u3Kwmsdo3hiNE43z9pX9","annotationValue":"hour","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000032","termSource":""}]}],"version":7}},"success":true}