{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lucie Pfeiferova"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-10278"],"description":["In this in-vitro study, we demonstrate the different effects of exosomes produced by melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of CMM. Both normal and cancer-associated fibroblast were prepared by a)DMEM with 10% EDS (control); b) DMEM with 10% Exosome-depleted serum (EDS) + 10 microg/ml G-361 exosomes (EXO_G361); c) DMEM with 10% EDS + 10 microg/ml exosomes from FBS (EXO_FBS). The cells were cultured for 72 hours. Transcriptome analysis was performed 72 hours after exosome application. Total RNA was isolated using RNeasy Micro Kit (Qiagen)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Samples were inoculated in DMEM with 10% FBS for 24 hours. After that time, samples were cultured for 72 hours in a) DMEM with 10% Exosome depleted serum (EDS) [control]; b) DMEM with 10% EDS + 10 microg/ml G-361 exosomes [EXO_G361]; c) DMEM with 10% EDS + 10 microg/ml exosomes from FBS [EXO_FBS].","Sequencing - Libraries were sequenced on the Illumina NextSeq® 500 platform (Illumina) using 75bp single-end configuration. The sequencing yielded on average 30 million reads per sample.","Nucleic Acid Extraction - Total RNA was isolated by the Qiagen RNeasy Micro Kit (Qiagen), according to the manufacturer's protocol, including treating samples by DNase I.","Library Construction - For the library construction, KAPA mRNA HyperPrep Kit with Poly(A) mRNA selection (Roche) was used with starting amount of 1000 ng of total RNA."],"figure_sub":["MIAME Score","Organization","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - ---","Sequence Alignment - Technical quality control and gene quantification were done using the nf-core/rnaseq v2.0 bioinformatics pipeline (Ewels et al. 2020), with HISAT2 mapping (Kim et al. 2015) and featureCounts read counting (Liao et al. 2014). GRCh38 (Ensembl assembly version 95) was chosen as the reference genome (Yates et al. 2020). Technical quality control and gene quantification were done using the nf-core/rnaseq v1.4.2 bioinformatics pipeline (Ewels et al, 2020)with HISAT2 mapping (Kim et al, 2015) and Salmon quantification (Patro et al, 2017) GRCh38 (Ensembl assembly version 101) was selected as the reference genome (Yates et al, 2020). A raw count matrix (merged_gene_counts_featurecounts.txt) has been provided."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_authors":["Karolina Strnadova","Lukáš Lacina","Karel Smetana","Lucie Pfeiferova"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of fibroblasts influenced by exosomes derived from melanoma cell line G-361","description":"In this in-vitro study, we demonstrate the different effects of exosomes produced by melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of CMM. Both normal and cancer-associated fibroblast were prepared by a)DMEM with 10% EDS (control); b) DMEM with 10% Exosome-depleted serum (EDS) + 10 microg/ml G-361 exosomes (EXO_G361); c) DMEM with 10% EDS + 10 microg/ml exosomes from FBS (EXO_FBS). The cells were cultured for 72 hours. Transcriptome analysis was performed 72 hours after exosome application. Total RNA was isolated using RNeasy Micro Kit (Qiagen).","dates":{"release":"2022-12-31T00:00:00Z","modification":"2025-05-20T08:43:34.15Z","creation":"2025-05-20T08:43:34.15Z"},"accession":"E-MTAB-10278","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}