{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Florian Finkernagel"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14411"],"description":["Human peritoneal mesothelial cells (HPMCs) were incubated with the conditioned media collected from tumor cells genetically modified to inducibly overexpress BCAM."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - STAR 2.7.1d onto Ensembl 96. BAM files were anonymized with BAMBoozle."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Florian Finkernagel","Suresh Sivakumar","Rolf Müller"],"additional_accession":[]},"is_claimable":false,"name":"Human peritoneal mesothelial cell response to conditioned media of BCAM overexpressing OVCAR8 cells (inducible overexpression)","description":"Human peritoneal mesothelial cells (HPMCs) were incubated with the conditioned media collected from tumor cells genetically modified to inducibly overexpress BCAM.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:14.884Z","creation":"2024-09-03T16:59:58.25Z"},"accession":"E-MTAB-14411","cross_references":{"Biostudies":["E-MTAB-14412"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}