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The animals were housed in the JAXA Habitat Cages Units (HCU) located in the Kibo centrifuge hardware Cell Biology Experimental Facility on ISS. The 24 flight mice were subdivided into four groups. The first group of flight mice (n equals 6) were exposed to ambient microgravity conditions (MG group), the second and third groups of flight mice (n equals 6) were exposed to continuous AG of 0.33G and 0.67G respectively, and the fourth group was exposed to continuous 1G. AG was achieved through the use of a short-arm centrifuge for the duration of their stay on the ISS. The rotation rate for generating 0.33G, 0.67G, and 1.0G were 44 rpm, 63 rpm, and 77 rpm, respectively. The flight mice were then splashed down in the Atlantic Ocean on April 15, 2023 and returned to Earth alive. 12 Habitat Ground Control (HGC) mice were maintained in similar habitat conditions as the FLT mice exposed to 1G, inside the ISSES Chambers of operations conducted with a 3-day delay. The spaceflight mice were then euthanized and their eyes were removed and prepared for analysis. All mice received the same ad libitum access to food and water. Animal experiments were approved by the Institutional Animal Care and Use Committee of the University of Tsukuba, Explora Biolabs, JAXA and NASA. No protocol was required from The Loma Linda University (LLU) Institutional Animal Care and Use Committee (IACUC), since only archived frozen and fixed tissues were obtained after euthanasia. The research with vertebrate animals was done in strict accordance with guidelines and applicable laws in Japan and the United States of America.","name":"Animal Husbandry","parameters":[{"@id":"#139820171834896","parameterName":{"@id":"dLYAVygHOh0kgkpNueBLjd61fJm88B7XuVf9mcXt","annotationValue":"habitat","comments":[],"termAccession":"http://purl.obolibrary.org/obo/ENVO_01000739","termSource":""}},{"@id":"#139820171834416","parameterName":{"@id":"ZjmSSbPuCF9KW9S9qrQGc9mjnHs9TzHb1bMgnKcX","annotationValue":"duration","comments":[],"termAccession":"http://www.ebi.ac.uk/efo/EFO_0000433","termSource":"EFO"}},{"@id":"#139820171835472","parameterName":{"@id":"836pqVl5ANxhxWmhGfagwV444XEbE85timdrfTPa","annotationValue":"Body Weight at Launch","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820171834992","parameterName":{"@id":"QraHOmTwDKeoAzQ4qV8YkHG42OwaUEmQEmnFZeeT","annotationValue":"Diet","comments":[],"termAccession":"http://purl.bioontology.org/ontology/MESH/D004032","termSource":"MESH"}},{"@id":"#139820171835520","parameterName":{"@id":"wnjgyTd8rj1O0Oqecf2wG5bXCMq8VGJ9M4evlXyk","annotationValue":"Feeding Schedule","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820171835568","parameterName":{"@id":"wU8HV0MjusT6E4b8LvZKgeUuQFCbtMBF5AoRz4Ts","annotationValue":"light cycle","comments":[],"termAccession":"http://purl.obolibrary.org/obo/NCIT_C90419","termSource":"NCIT"}},{"@id":"#139820171837056","parameterName":{"@id":"rUITC4ow9EhLnBplmrRIKZM8QdQqMseWK2WN4Tz6","annotationValue":"Enrichment material","comments":[],"termAccession":"http://dicom.nema.org/resources/ontology/DCM/127190","termSource":""}}],"protocolType":{"@id":"fgJeaqjSqJ5cyOD3RghriGtovFjzXu5ilV043prU","annotationValue":"Animal Husbandry","comments":[],"termAccession":"http://purl.bioontology.org/ontology/MESH/D000822","termSource":""},"uri":"","version":""},{"@id":"#139820171833648","comments":[],"components":[],"description":"Within 6 hours of splashing down, mice were euthanized and their eyes were harvested. The left eyes from each experimental group were fixed in 4% paraformaldehyde in phosphate buffered saline (PBS) for immunohistochemistry (IHC) assays. The retina and optic nerve of the right eyes were dissected out from the eye globe and placed individually in sterile cryovials, snap frozen in liquid nitrogen and kept at -80C prior to use.","name":"sample collection","parameters":[{"@id":"#139820171836960","parameterName":{"@id":"eUm691aR7an5kII9bYi7JOSQEcghOzzbVfEjAtOG","annotationValue":"Sample Preservation Method","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139820171833888","parameterName":{"@id":"vbrzINCaNhslTc1WulmcigpF6afqM7x3H1PCAdm0","annotationValue":"Sample Storage Temperature","comments":[],"termAccession":"https://genelab-data.ndc.nasa.gov/","termSource":""}},{"@id":"#139820168094720","parameterName":{"@id":"FE8lRzLqFkigAbS8FvgiLevjkHJe0bSq27HMQoVJ","annotationValue":"Body Weight at Euthanasia","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168095440","parameterName":{"@id":"5rwTh6c63aAm9zauPOpJJV7IjyAjc5woSpwEDT72","annotationValue":"Euthanasia Method","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":"NCIT"}},{"@id":"#139820168097744","parameterName":{"@id":"oAsjGOgEqTfWF2wfmtxS6Gcr7hYI1ETT3CEZVbT8","annotationValue":"Age at Euthanasia","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168096880","parameterName":{"@id":"4HDey7Y6U4ckNywIfum9UFWduNLF0GD4sIp6jshP","annotationValue":"Euthanasia Date","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168094768","parameterName":{"@id":"oNvSozFvXTiSBweVqR8KqzpwPT4CQT53knWD4qu7","annotationValue":"BSP Dissection Date","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"zaKRMPLXOBudyE1ROMNBjnZXViwkiB6PT7wea0yd","annotationValue":"sample collection","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#139820170568704","comments":[],"components":[],"description":"RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA) following GeneLab SOP 3.1-Qiagen AllPrep DNA/RNA Mini with Qiagen RNase-Free DNase set (<a href=\"https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs\" target=\"_\" >https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs</a>). Homogenization buffer for RNA purification was made by adding 1:100 beta-mercaptoethanol to Buffer RLT (Qiagen, Valencia, CA) and kept on ice until use. MHU-8 retina tissues processed in this experiment were not weighted before extractions to avoid thaw and 900uL of cold homogenization buffer was added directly into the tissue tubes. Homogenization was performed using rotor stator homogenizer (Polytron, Raymertown, NY), 3 repetitions of 10 seconds each at speed of 21,000 per SOP 2.2-Tissue homogenization Using Polytron Rotor Stator Homogenizer (<a href=\"https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs\" target=\"_\" >https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs</a>). Homogenates were centrifuged for 5 minutes at RT and 14,000g to remove cell debris. The supernatant from each sample was then used to isolate and purify DNA and RNA following the manufacturer protocol. RNA was eluted in 40uL RNAse free H2O, and DNA was eluted in 40uL RNAse free H2O. Concentration for all RNA samples were measured using Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA) with Qubit RNA BR kit following SOP 4.1-RNA/DNA/miRNA/cDNA Quantification using Qubit Fluorimeter (<a href=\"https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs\" target=\"_\" >https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs</a>). RNA quality was assessed using the Agilent 4200 TapeStation with the Agilent RNA ScreenTape (Agilent Technologies, Santa Clara, CA). DNA quality and size were assessed using the Agilent 4200 TapeStation with Agilent gDNA ScreenTape Kit (Agilent Technologies, Santa Clara, CA). RNA integrity number equivalent (RINe) values are reported.","name":"Nucleic Acid Extraction","parameters":[{"@id":"#139820170570864","parameterName":{"@id":"Hop5C9AJDN9g3VYqtIJtB2A611oQjKFpzG6shAoZ","annotationValue":"QA Instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#139820170570432","parameterName":{"@id":"AKFULPaZzL2J22DNBTdtRb681TVpFMeJj3ziEprY","annotationValue":"QA Assay","comments":[],"termAccession":"","termSource":""}},{"@id":"#139820170567840","parameterName":{"@id":"g8azbwSqAA7koUkxl7Hlg5Uvzjh6wB5GG6CeIxyb","annotationValue":"QA Score","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"hvmnimkOSUuDnRXoMCmOVO622eV9H3rhB5Orz2Zc","annotationValue":"Nucleic Acid Extraction","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#139820170569760","comments":[],"components":[],"description":"ERCC ExFold RNA Spike-In Mixes (Thermo Fisher Scientific, Waltham, MA, Cat 4456739, v92), Mix 1 or Mix 2, were added on the day of library prep at the concentrations suggested by the manufacturer protocol. SOP 5.2 Use of ERCC Spike-In Mixes and UMRR/UHRR Controls for Total RNA Sequencing (<a href=\"https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs\" target=\"_\" >https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs</a>).","name":"Spike-in Protocol","parameters":[{"@id":"#139820170569424","parameterName":{"@id":"urtYVn1xrJoyWgVLevPXJe6JED4C9gn7QTqgos0a","annotationValue":"Spike-in Quality Control","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820170568656","parameterName":{"@id":"ogxZESVz5mGfjvt4pVcI4kQFNewTo1wXhEY6hacF","annotationValue":"Spike-in Mix Number","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"DO2mBkJ1DsCJHyQ8iKIzaV3xMvSogV9oNFPivY71","annotationValue":"spike-in protocol","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""},"uri":"","version":""},{"@id":"#139820170568368","comments":[],"components":[],"description":"RNA ribo depletion and library preparation was done with Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina Inc., San Diego, CA). Input RNA was approximately 100nG with RIN greater than 4. Sample FLT17 and FLT02 input was below 30ng. Unique dual index adapters (Illumina Inc., San Diego, CA) were used, and 12 cycles PCR were performed. Library fragment size was assessed using Agilent 4200 TapeStation with D1000 DNA ScreenTape (Agilent Technologies, Santa Clara, CA) following GeneLab SOP 6.3 Quality analysis of sequencing libraries using 4200 TapeStation System with D1000 reagent kit (<a href=\"https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs\" target=\"_\" >https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs</a>). Pooled library concentration was measured by Qubit 4 Fluorometer (ThermoFisher Scentific, Waltham, MA) following SOP 4.1-RNA/DNA/miRNA/cDNA Quantification using Qubit Fluorimeter (<a href=\"https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs\" target=\"_\" >https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs</a>). Library quality assessment was performed on iSeq100 (Illumina, San Diego, CA).","name":"Library Construction","parameters":[{"@id":"#139820170571248","parameterName":{"@id":"SXpkstgzgf9WOhn8BRUImqf5kbHf1TJ3GjkLiaMg","annotationValue":"Library Selection","comments":[],"termAccession":"","termSource":""}},{"@id":"#139820149853104","parameterName":{"@id":"rlzTK2chbZkUcaCWHWpzFmlVUzKNZ7DXWAzUXMTb","annotationValue":"Library Layout","comments":[],"termAccession":"","termSource":""}},{"@id":"#139820149852864","parameterName":{"@id":"FgvdSWC3uI17LsXvErGgSgUHhsklR2Ok3RnEeJgE","annotationValue":"Stranded","comments":[],"termAccession":"","termSource":""}},{"@id":"#139820149851520","parameterName":{"@id":"ySR21dzJk0nfv7KlUyMLi1BCCpZs50alfaupJ80l","annotationValue":"Library Batch Number","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820149852576","parameterName":{"@id":"8WYoCyz2C7EHCUeJopWqPTSkwz6WD98uPi77l4Ik","annotationValue":"Library Kit","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"jlgnONtnl1cbnUwKKehnj9aCWkaf8ZPvhHTdzhV8","annotationValue":"Library Construction","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#139820170567984","comments":[],"components":[],"description":"RNA sequencing was performed by GeneLab Sample Processing Lab on Illumina NovaSeq 6000. Sequencing was set up as following: Read 1: 151 bp, Index1: 17 bp, Index2: 8 bp Read 2: 151 bp. PhiX included as control and to increase library diversity. Protocol followed is SOP 7.1-Setting up NovaSeq 6000 and iSeq 100 Sequencers (<a href=\"https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs\" target=\"_\" >https://github.com/nasa/GeneLab-sampleProcessing/tree/master/SOP_pdfs</a>).","name":"Nucleic Acid Sequencing","parameters":[{"@id":"#139820149850800","parameterName":{"@id":"QZv3O6FfjrX7Rj1AdVBpE7MMkvX0gDPFNyhTgsul","annotationValue":"Sequencing Instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#139820149851568","parameterName":{"@id":"CtQ18ML4iL8up3q8jIQxtenGoYSNWw4i3XMQYFwU","annotationValue":"Base Caller","comments":[],"termAccession":"","termSource":""}},{"@id":"#139820149853728","parameterName":{"@id":"DOWz9RyvfMoltYGyC7An2WqtHdVXvLLJU32JiRbM","annotationValue":"Read Length","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":"NCIT"}}],"protocolType":{"@id":"vbHeywu5lMpfsh3jNyY18mRWy5aZupc8gVSXD5Uh","annotationValue":"Nucleic Acid Sequencing","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#139820170568512","comments":[],"components":[],"description":"Raw fastq files were assessed for % rRNA using HTStream SeqScreener (version 1.3.2) and filtered using Trim Galore! (version 0.6.7) powered by Cutadapt (version 3.7). Raw and trimmed fastq file quality was evaluated with FastQC (version 0.11.9), and MultiQC (version 1.12) was used to generate MultiQC reports. Mus musculus STAR and RSEM references were built using STAR (version 2.7.10a) and RSEM (version 1.3.1), respectively, Ensembl release 107, genome version GRCm39 (Mus_musculus.GRCm39.dna.primary_assembly.fa) concatenated with ERCC92.fa from ThermoFisher (<a href=\"https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\" target=\"_\" >https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip</a>), and the following gtf annotation file: Mus_musculus.GRCm39.107.gtf concatenated with the ERCC92.gtf file from ThermoFisher (<a href=\"https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\" target=\"_\" >https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip</a>). Trimmed reads were aligned to the Mus musculus + ERCC STAR reference with STAR (version 2.7.10a) and aligned reads were assessed for strandedness using RSeQC Infer Experiment (version 4.0.0) then aligned reads from all samples were quantified using RSEM (version 1.3.1), with strandedness set to reverse. Quantification data was imported to R (version 4.1.3) with tximport (version 1.22.0) and normalized with DESeq2 (version 1.34.0) median of ratios method. Normalized gene counts were subject to differential expression analysis. Differential expression analysis was performed in R (version 4.1.3) using DESeq2 (version 1.34.0); 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 following Bioconductor and annotation packages: STRINGdb (v2.8.4), PANTHER.db (v1.0.11), and org.Mm.eg.db (v3.15.0).","name":"Sequence Analysis Data Transformation","parameters":[{"@id":"#139820149852288","parameterName":{"@id":"lwanqOYhlZ3TgheWeidAVorCRpt0kYAfJlfldbj0","annotationValue":"User Submitted Raw Counts Tables","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820149851184","parameterName":{"@id":"ohLPWNgBX1m1IDAO5bT1zOActvuC0uXohHZWildF","annotationValue":"User Submitted Normalized Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820149852816","parameterName":{"@id":"OCCuF0zlUBL2M6BMndL84UhzLQtlkfIpwcEbWOFd","annotationValue":"User Submitted differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"OBI"}}],"protocolType":{"@id":"1u1iAHACjRWahy7RlUcQ1PsaeY4wLCWYiGYYNdDU","annotationValue":"Sequence Analysis Data Transformation","comments":[],"termAccession":"","termSource":"OBI"},"uri":"","version":""},{"@id":"#139820170571536","comments":[],"components":[],"description":"Fastq format was checked with fastq_utils v0.25.1. Quality assessment of reads was performed with FastQC v0.12.1 and reports were combined with MultiQC v1.26. rRNA percentages of reads were estimated with the 'hts_SeqScreener' program of htstream v1.3.3 screened against a fasta file of Mus-musculus rRNA sequences retrieved from NCBI on 01-Sep-2021.","name":"GeneLab raw data processing protocol","parameters":[{"@id":"#139820176359920","parameterName":{"@id":"Ohs1BbENFJo4CWnwszKmpZ4g1nZJNqqJv60k0wyP","annotationValue":"Read Depth","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":"NCIT"}},{"@id":"#139820176361024","parameterName":{"@id":"ahid9PluC4PDyLrGsFf76ktvkDjjMpBswqDNjOZA","annotationValue":"MultiQC Data Files","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820176363232","parameterName":{"@id":"RaWNd099ZqS9NO9TqfvpU9arANv1Do2iAJueQJMm","annotationValue":"rRNA Contamination","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""},{"@id":"#139820149851952","comments":[],"components":[],"description":"Data were processed as described in GL-DPPD-7101-G (<a href=\"https://github.com/nasa/GeneLab_Data_Processing/blob/master/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md\" target=\"_\" >https://github.com/nasa/GeneLab_Data_Processing/blob/master/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md</a>), using NF_RCP version 2.0.2 (https://github.com/nasa/GeneLab_RNASeq_Workflow/tree/NF_RCP_2.0.2). In short, raw fastq files were filtered using Trim Galore! (version 0.6.10) powered by Cutadapt (version 4.2). Trimmed fastq file quality was evaluated with FastQC (version 0.12.1), and MultiQC (version 1.26) was used to generate MultiQC reports. Mus Musculus STAR and RSEM references were built using STAR (version 2.7.11b) and RSEM (version 1.3.3), respectively, Ensembl release 112, genome assembly GRCm39 (Mus_musculus.GRCm39.dna.primary_assembly.fa) concatenated with ERCC92.fa from ThermoFisher (<a href=\"https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\" target=\"_\" >https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip</a>), and the following gtf annotation file: Mus_musculus.GRCm39.112.gtf concatenated with the ERCC92.gtf file from ThermoFisher (<a href=\"https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\" target=\"_\" >https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip</a>). Trimmed reads were aligned to the Mus Musculus + 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. 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.Mm.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":"#139820168094192","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002569","termSource":"OBI"}},{"@id":"#139820168094240","parameterName":{"@id":"s2HskUjUzSQmahcRYDfv1xBVjYScvewE8EO773hd","annotationValue":"Trimmed Sequence Data/Trimming Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168095344","parameterName":{"@id":"Paz4Pjo6sV6E66RG3a9xuZDjKKpk7ywwq3VwmAwn","annotationValue":"Trimmed Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168096976","parameterName":{"@id":"lqpWRJZ7O2rPhdA4uPNANCqeFig4cQhw07RfB2f5","annotationValue":"aligned sequence data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002580","termSource":"OBI"}},{"@id":"#139820168096928","parameterName":{"@id":"SPhWEr1D3r2VJ9OKO5b94MEY02Ipod6UwkLtQaRk","annotationValue":"Aligned Sequence Data/Unmapped Reads","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168096064","parameterName":{"@id":"3AwnKZQDUPRaMntinM9bvBrGHpnb8qc6GaaZRIQh","annotationValue":"Aligned Sequence Data/Alignment Logs","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168097456","parameterName":{"@id":"ib7AEGeVUoAruCpz91Qn6GXdO3E5d8k0DSeT2EQR","annotationValue":"Aligned Sequence Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168097168","parameterName":{"@id":"QcbiokEiY9OO2PO8IXfNhCwNUeMq4JM2ugyguLO3","annotationValue":"RSeQC/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168094480","parameterName":{"@id":"CzV3xNixKDCRnULWE97WbT9v456v77sgf4dPZG0Y","annotationValue":"Raw Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168094288","parameterName":{"@id":"WXhsQG8JLZ5oK8kUYbPxGSfXi520yz8A4dEHcBKs","annotationValue":"Raw Counts Tables","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168094336","parameterName":{"@id":"w31o7Q91WYOVYIwRCqOCvdUs4H84WG2M5y8Qgu1N","annotationValue":"Raw Counts Data/MultiQC Reports","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168097120","parameterName":{"@id":"Lns3jxVPjBQ2dUuFO7KyPzSqST1hCHcuYbzwld4i","annotationValue":"Normalized Counts Data","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#139820168096736","parameterName":{"@id":"c4UoiNar4sA4ty0VawH08rhaf4AR7F8drWBP91tt","annotationValue":"differential expression analysis data","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0002584","termSource":"OBI"}},{"@id":"#139820168096016","parameterName":{"@id":"RU82pDdGEcbsiezMzkaKgjf1MKkk9FaQCjynpZUS","annotationValue":"ERCC Analyses","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"gHRCpX8ZCZrvMb1jv0PpSihU4DurynDUUnkOSfet","annotationValue":"data transformation","comments":[],"termAccession":"http://purl.obolibrary.org/obo/OBI_0200000","termSource":"OBI"},"uri":"","version":""}],"publicReleaseDate":"06-Nov-2024","publications":[],"studyDesignDescriptors":[],"submissionDate":"12-Aug-2024","title":"Artificial Gravity Attenuates the Transcriptomic Response to Spaceflight in the Optic Nerve and Retina -- Retina data","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":"BFtmHv7jE1g1SEfuffoEIGHvLtR5icFOjFbLPFs8","annotationValue":"gram","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000021","termSource":""},{"@id":"1elCZM8nktXBnEgzvNbC6OfVMVRCjhLVI3KdVQv4","annotationValue":"week","comments":[],"termAccession":"http://purl.obolibrary.org/obo/UO_0000034","termSource":""}]}],"version":5}},"success":true}