{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Bjorn Baselet"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14151"],"description":["The goal of this study was to isolate CD4+ T cells  from the blood of healthy volunteers and expose them to simulated space stressors in a single and combined manner to investigate their effects on T cell activation, gene expression, and cytokine production. Cytokine levels for Th1, Th2, and Treg cell populations were measured using multiplex Luminex assays to assess functional changes in T cell subsets under simulated space conditions. Furthermore, this study aimed to analyze gene expression patterns using RNA-seq to identify key genes and pathways involved in T cell activation and the immune response that are significantly altered in response to simulated space conditions. Proteomic analysis was also conducted to examine changes in protein expression and modifications that may occur in CD4+ T cells under simulated space conditions. Overall, this study aimed to provide a comprehensive understanding of the effects of simulated space conditions on CD4+ T cells and their role in the immune response."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - 21 healthy male volunteers who met the inclusion criteria (see supplementary materials) were selected for this study. Blood samples were collected in 9mL lithium heparin tubes (Vacuette, Greiner Bio-One GmbH, Kremsmunster, Austria). Hematological analysis was performed using a Sysmex XS-800i automated hematology analyzer (Sysmex Corporation, Kobe, Japan). The instrument was calibrated and operated according to the manufacturer's instructions. CD4+ T cells were isolated by negative selection with RosetteSep Human CD4+ T Cell Isolation Kits (StemCell Technologies, Inc. Vancouver, BC, Canada) with a purity of 90 to 95% and according to the manufacturer's instructions. The isolated CD4+ T cells were cryopreserved in heat inactivated fetal bovine serum (HI FBS) with 10% DMSO for later use in the experimental procedures. Flow cytometry analysis was performed to confirm the purity of isolated CD4+ T cells using a gating strategy based on the expression of CD3 and CD4 markers. (see supplementary materials)   Upon thawing, cryopreserved CD4+ T cells were stimulated with an anti-CD3/CD28 stimulation cocktail from StemCell Technologies at a concentration of 1 μg/mL in complete T cell expansion medium (StemCell Technologies, Inc. Vancouver, BC, Canada). The cells were then divided into experimental groups. Stimulated CD4+ T cells were incubated at 37 °C with 5% CO2 for 24 h to allow for maximum activation and cytokine secretion, without compromising on cell viability. Figure 2 provides a schematic overview of the experimental design.","Nucleic Acid Extraction - Total RNA was extracted from isolated CD4+ T cells using the RNeasy Plus Mini Kit (Qiagen, Germany), according to the manufacturer’s protocol. RNA integrity was assessed using the Agilent RNA 6000 Pico Kit and 2100 BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA, USA). The RNA integrity number (RIN) values are shown in the Supplementary materials. For all samples, the RIN values met the requirements for high-quality RNA-sequencing analysis.","Library Construction - Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first-strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using either dUTP for the directional library or dTTP for the non-directional library. The non-directional library was prepared after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The directional library was prepared after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time polymerase chain reaction (RT-PCR) for quantification and a bioanalyzer for size distribution detection.","Sequencing - Quantified libraries were pooled and sequenced on Illumina platforms according to the effective library concentration and data amount."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Bjorn Baselet","Emre Etlioglu"],"additional_accession":[]},"is_claimable":false,"name":"Effects Of Simulated Space Conditions On CD4+ T Cells: A Multi Modal Analysis","description":"The goal of this study was to isolate CD4+ T cells  from the blood of healthy volunteers and expose them to simulated space stressors in a single and combined manner to investigate their effects on T cell activation, gene expression, and cytokine production. Cytokine levels for Th1, Th2, and Treg cell populations were measured using multiplex Luminex assays to assess functional changes in T cell subsets under simulated space conditions. Furthermore, this study aimed to analyze gene expression patterns using RNA-seq to identify key genes and pathways involved in T cell activation and the immune response that are significantly altered in response to simulated space conditions. Proteomic analysis was also conducted to examine changes in protein expression and modifications that may occur in CD4+ T cells under simulated space conditions. Overall, this study aimed to provide a comprehensive understanding of the effects of simulated space conditions on CD4+ T cells and their role in the immune response.","dates":{"release":"2025-06-01T00:00:00Z","modification":"2024-06-06T10:10:18.63Z","creation":"2024-06-06T10:10:18.63Z"},"accession":"E-MTAB-14151","cross_references":{"ENA":["ERP160915"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}