biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsDominik HadzegamicroRNA profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17459This miRNA microarray experiment is part of the same multi-omics study as the RNA-seq and whole-exome sequencing data deposited in the European Nucleotide Archive under accession PRJEB122863. The aim of this study was to identify prognostic molecular signatures for GTC patients derived from comprehensive molecular characterization of cisplatin-resistant variants of established GCT cell lines. GCT cell lines and their isogenic cisplatin-resistant variants (2102Ep, NCCIT, NT2, JAR, JEG3, NOY1, NCR-G1, and TCam2) were profiled by RNA-, microRNA-, and whole-exome sequencing (WES).biostudies-arrayexpressScaning - Microarray slides were scanned at a resolution of 3 µm using an Agilent SureScan Microarray Scanner G5761A. TIFF images were processed using Agilent Feature Extraction Software version 12.0.3.2 with the array design file 070156_D_F_20141006.xml. Feature Extraction generated raw feature-level signal intensities and quality-control metrics for the single-colour green channel. The resulting raw signal data were subsequently imported into GeneSpring software for downstream analysis.Sample Treatment - Cisplatin-resistant variants were derived from their corresponding cisplatin-sensitive parental germ cell tumour cell lines by long-term or repeated exposure to increasing sub-lethal concentrations of cisplatin. Resistant variants generated by the Slovak group were established by continuous propagation in cisplatin for approximately 6 months without recovery periods. Cells were initially exposed to 0.165 µM cisplatin, and the concentration was gradually increased to 0.33 µM. The resulting resistant variants were subsequently maintained in medium containing 0.33 µM cisplatin. Resistant variants designated DE or NL were generated by repeated exposure to increasing sub-lethal cisplatin concentrations with intermittent recovery periods. Variants designated CR were established by exposure to increasing cisplatin concentrations over approximately 20 months, starting at 0.1 µM. When approximately 80% lethality was reached, cells were allowed to recover for four passages without cisplatin before further dose escalation. Corresponding parental cell lines were maintained under the same general culture conditions without selection for cisplatin resistance.Hybridization - Cy3-pCp-labelled RNA samples were loaded onto Agilent SurePrint Human miRNA Microarrays, Release 21.0, Design ID 070156. Hybridization was performed in an Agilent hybridization oven for 20 h at 55 °C with rotation at 20 rpm. Following hybridization, the slides were washed using Agilent Gene Expression Wash Buffers according to the manufacturer's instructions.Growth Protocol - Human germ cell tumour cell lines were maintained in either RPMI 1640 medium or high-glucose DMEM containing 4.5 g/L glucose, according to the requirements of the individual cell line. Culture media were supplemented with 10% fetal bovine serum, penicillin, streptomycin and amphotericin; DMEM cultures were additionally supplemented with 2 mM glutamine. Cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2. Cell line identities were confirmed by short tandem repeat profiling, and cultures were routinely screened for mycoplasma contamination.Sample Collection - Exponentially growing cells were harvested by centrifugation. Cell pellets were prepared from approximately 2 × 10^6 cells, washed with 1 mL of ice-cold phosphate-buffered saline (PBS), and centrifuged at 1,200 rpm for 5 min. The resulting pellets were preserved in 500 µL of DNA/RNA Shield (Zymo Research, Irvine, CA, USA) and stored at −20 °C until nucleic acid extraction.Labeling - A total of 100 ng of total RNA was dephosphorylated and labelled by ligation with Cyanine 3-pCp (Cy3-pCp) using the Agilent miRNA Complete Labeling and Hybridization Kit according to the manufacturer's instructions. Labelled RNA was purified using Micro Bio-Spin P-6 Gel Columns (Bio-Rad, USA). The desalted labelled samples were dried in a vacuum concentrator and subsequently resuspended in the supplied hybridization mixture.Nucleic Acid Extraction - Total RNA was extracted using the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructions. RNA concentration was measured using a NanoDrop 1000 spectrophotometer and the RNA Broad Range Assay on a Qubit fluorometer. Samples with insufficient RNA concentration were concentrated using the RNA Clean & Concentrator-5 Kit (Zymo Research). RNA integrity was assessed using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit. Only samples with an RNA integrity number (RIN) greater than 8 were used for microarray analysis.MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsLucia KucerovaDominik HadzegaMichal MegoAndrea SoltysovafalseCis-platin resistant cell lines and sensitive parental cell lines: microRNA profiling by arrayThis miRNA microarray experiment is part of the same multi-omics study as the RNA-seq and whole-exome sequencing data deposited in the European Nucleotide Archive under accession PRJEB122863. The aim of this study was to identify prognostic molecular signatures for GTC patients derived from comprehensive molecular characterization of cisplatin-resistant variants of established GCT cell lines. GCT cell lines and their isogenic cisplatin-resistant variants (2102Ep, NCCIT, NT2, JAR, JEG3, NOY1, NCR-G1, and TCam2) were profiled by RNA-, microRNA-, and whole-exome sequencing (WES).2026-08-14T00:00:00Z2026-08-14T01:00:45.659Z2026-08-04T11:55:43.084ZE-MTAB-17459EFO_0002944EFO_0003814EFO_0000753EFO_0003813EFO_0003789EFO_0005518EFO_0003815EFO_0003969