{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Mitra Gultom"],"organism":["Sus scrofa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15491"],"description":["In this study, we investigated the molecular and functional properties of genetically modified porcine aortic endothelial cells (PAECs) that carry a knockout of α1,3-galactosyltransferase and express human CD46 and thrombomodulin (3GM) in xenogeneic (Normal Human Serum alone) and inflammatory environments (TNF + Normal Human Serum), with Wild Type pig aortic endothelial cells as comparison."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Bulk RNA barcoding and sequencing (BRB-seq) was performed by Alithea Genomics. A total of 200 ng of cellular RNA from four independent biological replicates was used to generate BRB-seq libraries,according to the company's pipeline.","Sample Collection - To culture the the porcine endothelial cells using a microfluidic system, 100,000 cells in 100 μl of complete media were seeded in a μ-slide VI 0.4 (Ibidi, 80606) 16,21. Prior to seeding, the μ-slide was coated with 100 μl of 10 μg/ml fibronectin (Merck, FC010) for 30 min at 37 °C. Cells were incubated overnight before being connected to a peristaltic pump (Gilson, Minipuls 3) using sterile silicone tubings to introduce the flow. Flow media consisting of DMEM supplemented with 10% FBS, 1% glutamine, 1%BSA (Sigma, A7030), and 4% dextran (Sigma, 31390), was used as the flow medium. The laminar shear stress was adjusted to 10 dyn/cm2 and maintained for 72 h in a humidified incubator at 37 °C and with 5% CO2. The media was refreshed every day. For simulating xenogeneic activation, cells were perfused with 3 mL of flow media containing 10% pooled normal human serum (NHS) obtained from three healthy donors for 2 h. Additionally, cells were primed with 100 ng/ml recombinant human TNF-α (RnD Systems, 210-TA-020) for 4 h, prior to NHS perfusion, to simulate the inflammatory conditions in xenotransplantation settings.","Nucleic Acid Extraction - Total cellular RNA from the all porcine endothelial samples was isolated using the NucleoSpin RNA kit (Macherey-Nagel, 740955) according to the manufacturer’s guidelines, followed by quantification of the total RNA with a Quantifluor RNA system (Promega, E3310).","Sequencing - Sequencing was performed by Alithea genomics on an Illumina HiSeq 4000 platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - For gene expression analysis, the raw counts were normalized and log1P transformed using the DESeq2 package (version 4.3.0). analysis  was performed using a variety of additional packages in R (Version 2025.05.1 +513)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["BRB-seq tool and pipeline","Gilson Minipuls 3","Illumina HiSeq 4000","Macbook Pro 2018","NucleoSpin RNA kit (Macherey-Nagel)"],"study_type":["RNA-seq of coding RNA"],"species":["Sus scrofa"],"pubmed_authors":["Mitra Gultom"],"additional_accession":[]},"is_claimable":false,"name":"Cellular dynamics of transgenic porcine endothelial cells to inflammatory stimuli in xenotransplantation settings","description":"In this study, we investigated the molecular and functional properties of genetically modified porcine aortic endothelial cells (PAECs) that carry a knockout of α1,3-galactosyltransferase and express human CD46 and thrombomodulin (3GM) in xenogeneic (Normal Human Serum alone) and inflammatory environments (TNF + Normal Human Serum), with Wild Type pig aortic endothelial cells as comparison.","dates":{"release":"2026-04-01T00:00:00Z","modification":"2026-04-02T01:05:04.419Z","creation":"2025-08-13T15:41:08.81Z"},"accession":"E-MTAB-15491","cross_references":{"ENA":["ERP178746"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}