biostudies-arrayexpressJiri NovotnyHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-10290In this in-vitro study, we demonstrated the different effects of exosomes produced by G361 melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of cutaneous malignant melanoma. Both normal and cancer-associated fibroblasts were cultivated in either DMEM with 10% EDS (exosome-depleted serum) (control) or DMEM with 10% EDS + 10 microg/ml G361 exosomes (EXO). The cells were harvested after 24 hours of cultivation.biostudies-arrayexpressSequencing - All single-cell RNA-sequencing was performed with an Illumina Nextseq 500 with the following setup: paired-end, read1 length 28bp, read2 length 54bp.Nucleic Acid Extraction - Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 4,000 cells. Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns PN-100026 was used.Sample Collection - Primary human fibroblasts were isolated from healthy juvenile trunk skin and cancer-associated fibroblasts were isolated from melanoma metastasis. The cells were treated without or with exosomes from G361 melanoma cell line (commercially available; CVCL_1220) in DMEM + 10% exosome depleted serum.Growth Protocol - Cell suspensions were inoculated in DMEM + 10% fetal bovine serum and cultured for 24 hours. After the medium was changed for DMEM + 10% exosome depleted serum without/with 10 ug/ml total concentration of exosomes from melanoma cell line G361. The cells were cultured for additional 24 hours.Library Construction - Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 4,000 cells. Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns PN-100026 was used.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw data from Illumina Nextseq 500 sequencer were processed by cellranger software (v4.0.0) provided by 10x Genomics. Cellranger mkfastq command was run on each replicate (i.e. each sequencing run).Data Transformation - Cellranger software (v4.0.0, reference transcriptome \\"refdata-gex-GRCh38-2020-A\\") provided by 10x Genomics was run (count command) on raw FASTQ files of both replicates. Raw feature barcode matrices were imported to SingleCellExperiment object in R statistical environment, empty droplets were removed by emptyDrops package (FDR < 0.01) and resulting barcode matrix was saved in TSV format.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNA from single cellsHomo sapiensMichal KolarKarolina StrnadovaLukas LacinaKarel SmetanaJiri NovotnyfalseSingle-cell RNA-seq of fibroblasts influenced by exosomes derived from melanoma cell line G361In this in-vitro study, we demonstrated the different effects of exosomes produced by G361 melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of cutaneous malignant melanoma. Both normal and cancer-associated fibroblasts were cultivated in either DMEM with 10% EDS (exosome-depleted serum) (control) or DMEM with 10% EDS + 10 microg/ml G361 exosomes (EXO). The cells were harvested after 24 hours of cultivation.2021-12-31T00:00:00Z2025-05-12T13:55:56.009Z2025-05-12T13:55:56.009ZE-MTAB-10290ERP128010E-MTAB-10278EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0003816EFO_0005518EFO_0004184