biostudies-arrayexpressFlorian FinkernagelHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14411Human peritoneal mesothelial cells (HPMCs) were incubated with the conditioned media collected from tumor cells genetically modified to inducibly overexpress BCAM.biostudies-arrayexpressSequencing - Sequencing was performed using Illumina NextSeq 550 v2.5 kits according to manufactures' protocol.Sample Collection - fter 48 hrs, the HPMCs were lysed with RA1 buffer for RNA isolation.Library Construction - “QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina” (Lexogen, Vienna, Austria)Growth Protocol - In brief, macroscopically tumor-free omentum was digested with trypsin for 30 min, followed by MACS depletion of CD45+ and EpCAM+ cells. Mesothelial cells were cultured in OCMI/5% FCS medium35 for a maximum of 3-5 passages. Human umbilical vein endothelial cells (HUVECs) were cultured using HUVEC Endothelial Growth Media (Cat. #C-22011, PromoCell; St. Louis, USA).Nucleic Acid Extraction - MN NucleoSpin RNA Isolation Kit according to manufacture's instructions.Sample Treatment - HPMCs are incubated with conditoned media for 48 hrs. Conditioned media: OVCAR-8 cells with disrupted BCAM alleles (BCAM_KO cells) 7 were transfected with the pTetOne vector (Takara Bio Europe; Saint-Germain-en-Laye, France; Cat. #634301) containing either BCAM1 (Transcript 1, Ref. Seq - NM_005581.4) or BCAM2 (Transcript 2, Ref. Seq - NP_001013275.1). The cells were co-transfected with a linear selection marker containing puromycin resistance, using the Xfect transfection reagent according to the manufacturer’s instructions. Cells were selected in the presence of puromycin (Sigma-Aldrich; Taufkirchen, Germany; Cat. #P8833) at a concentration of 0.25 µg/ml. Stable clones were then analyzed for BCAM expression by immunoblotting and FACS analysis. The clones were cultured in RPMI 1640 (Life Technologies; Darmstadt, Germany) supplemented with 10% Tet System Approved FBS (Takara Bio Europe; Saint-Germain-en-Laye, France; Cat. #631106) and 1% Penicillin-Streptomycin (Cat. #P0781, Sigma-Aldrich; Taufkirchen, Germany). For BCAM induction, cells were treated with doxycycline at a concentration of 1 µg/ml (Cat. #D9891-1G, Sigma-Aldrich; Taufkirchen, Germany). OVCAR8 cells were cultured in RPMI 1640 (Cat. #61870044, Thermo Fisher Scientific, Darmstadt, Germany) supplemented with 10% FBS (Cat. #FBS-LE-12A/RES1822, Capricon Scientific, Ebsdorfergrund, Germany). Cells were seeded in 10 cm dishes at a density of 3.5 × 10⁶ cells per dish, and the medium was replaced with serum-free medium after 24 hrs. BCAM-OE cells were incubated for an additional 48 hrs. CM was collected, centrifuged at 300xg for 5 min to remove dead cells, and further clarified by centrifugation at 1500xg for 5 min.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - STAR 2.7.1d onto Ensembl 96. BAM files were anonymized with BAMBoozle.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 550RNA-seq of coding RNAHomo sapiensFlorian FinkernagelSuresh SivakumarRolf MüllerfalseHuman peritoneal mesothelial cell response to conditioned media of BCAM overexpressing OVCAR8 cells (inducible overexpression)Human peritoneal mesothelial cells (HPMCs) were incubated with the conditioned media collected from tumor cells genetically modified to inducibly overexpress BCAM.2025-12-31T00:00:00Z2025-12-31T02:02:14.884Z2024-09-03T16:59:58.25ZE-MTAB-14411E-MTAB-14412EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969