{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Flóra Dr. Demeter"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15672"],"description":["This study performed transcriptional profiling of three independent human umbilical vein endothelial cell (HUVEC) lines derived from unique donors, each cultured in four different media formulations varying in basic composition, serum, and growth factor content. The aim was to evaluate the relative contributions of donor-specific genetic variation and culture conditions to endothelial transcriptomic profiles. Such an investigation is highly relevant, as primary endothelial cells (e.g., HUVECs) are widely used in basic research and drug development, yet published findings are often contradictory or difficult to reproduce."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - Samples were processed according to the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Kit protocol, using the Agilent Spike-In Kit as per the manufacturer's instructions. The detailed protocol is available at: https://www.agilent.com/cs/library/usermanuals/public/G4140-90050_GeneExpression_TwoColor_6.9.pdf.","Scaning - Post-hybridization, the microarrays were washed as per the manufacturer's protocol and scanned using an Agilent Microarray Scanner (G2505C) with 2 μm resolution and 20-bit color depth. The scanned images were processed and analyzed using Agilent GeneSpring 14.5-GX software.","Growth Protocol - HUVECs were grown in gelatin-precoated flasks (Corning® Costar®) in MCDB131 medium (Life Technologies) completed with 5% heat‑inactivated, fetal calf serum (FCS), 100U/ml Penicillin and 100 μg/ml Streptomycin antibiotics, 7.5 U/ml Heparin, 1% Chemically Defined Lipid Concentrate (Life Technologies), 1% Glutamax (Life Technologies),  5 µg/ml Ascorbic acid, 250 nM Hydrocortisone, 10 mM Hepes, 0.3% Insulin Transferrin Selenium (Life Technologies), 2 ng/ml human recombinant epidermal growth factor (R&D Systems), and 1 ng/ml human recombinant basic fibroblast growth factor (hereinafter: MCDB) until reaching full confluency. Experiments were performed on three independent primary HUVEC cultures from different individuals at passage 3 (namely HUVEC 1302/3, HUVEC 1309/3 and HUVEC 1314/3).","Nucleic Acid Extraction - Total RNA extraction was performed using the SPLIT RNA Extraction Kit (Lexogen), and analyzed on the Agilent Microarray platform. The RIN of all RNA samples were above 9.","Sample Collection - Confluent layers of three individual HUVEC lines (1302, 1309, 1314) were cultured in four cell culture media (EBM, HIMV, MCDB, MCDB-S) in 24-well plates for 1 days. HUVECs were washed with PBS, lysed and stored in TRI® reagent.","Sample Treatment - After reaching full confluency, HUVECs were seeded into 24-well plates and cultured for 24 h in a 50:50 mixture of MCDB and one of four media (EBM, HIMV, MCDB, or MCDB-S), followed by 24 h in 100% of the respective medium prior to mRNA isolation. EBM consisted of EBM-2 Basal Medium (Lonza) supplemented with 5% heat-inactivated FCS (PAN Biotech), 30 μg/ml gentamicin (Lonza), 15 ng/ml amphotericin (Lonza), 75 μg/ml ascorbic acid (Lonza), 0.2 μg/ml hydrocortisone (Lonza), 10 ng/ml hrEGF (Lonza), 4 ng/ml hrBFGF (Lonza), 2 ng/ml VEGF (Lonza), and 5 ng/ml R3-IGF-1 (Lonza). HIMV was AIM-V medium (Life Technologies) supplemented with 1% FCS (PAN Biotech), 50 μg/ml streptomycin, 10 μg/ml gentamicin, 7.5 U/ml heparin, 2 ng/ml hrEGF (R&D Systems), and 1 ng/ml hrBFGF. MCDB consisted of MCDB-131 medium (Life Technologies) supplemented with 5% FCS (PAN Biotech), 100 U/ml penicillin, 100 μg/ml streptomycin, 7.5 U/ml heparin, 1% Chemically Defined Lipid Concentrate (Life Technologies), 1% Glutamax (Life Technologies), 5 μg/ml ascorbic acid, 250 nM hydrocortisone, 10 mM HEPES, 0.3% Insulin Transferrin Selenium (Life Technologies), 2 ng/ml hrEGF (R&D Systems), and 1 ng/ml hrBFGF. MCDB-S was based on MCDB-131 medium (Life Technologies) supplemented with 1% FCS (PAN Biotech), 100 U/ml penicillin, 100 μg/ml streptomycin, 7.5 U/ml heparin, 1% Chemically Defined Lipid Concentrate (Life Technologies), 1% Glutamax (Life Technologies), 5 μg/ml ascorbic acid, 250 nM hydrocortisone, and 10 mM HEPES. Unless otherwise specified, reagents were obtained from Sigma Aldrich.","Hybridization - Equal amounts of Cyanine-3 (Cy3)-labeled or Cyanine-5 (Cy5)-labeled cRNA from samples were co-hybridized onto arrayed oligonucleotides on the same Agilent SurePrint G3 Human GE v3 8x60K (GPL21185) slide at 65 °C for 17 hours using the Agilent Gene Expression Hybridization Kit in SureHyb Hybridization Chambers (G2545A)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Flóra Dr. Demeter"],"data_protocol":["Data Transformation - Background subtraction and LOWESS normalization were performed using Agilent GeneSpring 14.5-GX. The aim of this study was to investigate genes with known functions; therefore, spots annotated only with LOC or XLOC identifiers, or lacking gene names, were excluded from the analysis. Fluorescence intensities of 14 housekeeping genes (RPLP0, PGK1, PPIA, SDHA, GAPDH, RPL13A, UBE2D2, HPRT1, YWHAZ, TFRC, ACTB, B2M, TBP, HMBS) were collected across 12 samples, and data were normalized to the average of the first 12 genes, which showed the lowest variability."],"additional_accession":[]},"is_claimable":false,"name":"Nature versus nurture: Genetic background and media composition shape endothelial cell transcriptomes in vitro","description":"This study performed transcriptional profiling of three independent human umbilical vein endothelial cell (HUVEC) lines derived from unique donors, each cultured in four different media formulations varying in basic composition, serum, and growth factor content. The aim was to evaluate the relative contributions of donor-specific genetic variation and culture conditions to endothelial transcriptomic profiles. Such an investigation is highly relevant, as primary endothelial cells (e.g., HUVECs) are widely used in basic research and drug development, yet published findings are often contradictory or difficult to reproduce.","dates":{"release":"2026-03-02T00:00:00Z","modification":"2026-05-31T00:03:16.578Z","creation":"2025-10-08T14:32:46.614Z"},"accession":"E-MTAB-15672","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003815","EFO_0003969"]}}