biostudies-arrayexpressClaudia PommerenkeHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16289Despite ethical concerns and scientific drawbacks, fetal bovine serum (FBS) remains a common supplement of culture media for continuous cancer cell lines. FBS alternatives like human platelet lysate (hPL) as well as animal-component free, chemically defined media (CDM) are commercially available for many years. Nevertheless, the acceptance of such alternative media is limited because data verifying the stability of the phenotype and function of a cell line in the alternative media are often lacking. Here, we have adapted four widely used human cancer cell lines (HELA, HL-60, JIMT-1, K-562) to hPL supplemented media and different CDM. To evaluate the suitability of the FBS-free replacements in comparison to the FBS media, we systematically analyzed the different cultures in respect to recovery after cryopreservation, STR-profiles, proliferation, morphology and their transcriptomes. Neither alterations in STR-profiles nor difficulties after cryopreservation were detected. With the exception of K-562, FBS-free cultures showed a reduced proliferation rate and, in some conditions, slight morphological alterations in comparison to FBS cultures. Transcriptome-wide GSEA indicated that culture media affected expression of genes involved in cholesterol homeostasis in all cell lines, and genes involved in epithelial-mesenchymal transition in HELA and JIMT-1. However, their overall phenotypes remained stable. Hematopoietic differentiation markers were among the differentially expressed genes of HL-60 and K-562 cultures, but their main phenotypes remained very similar which was further confirmed by successful induction of differentiation of HL-60 in FBS-free media. In summary, our multiparametric approach delivers validated data supporting the transition to FBS-free media for the analyzed cancer models.biostudies-arrayexpressNucleic Acid Extraction - Total RNA was extracted via miRNeasy Mini Kit (Qiagen, Hilden, Germany) including DNase digestion.Sequencing - The libraries were sequenced on NovaSeq 6000 (2x151 cycles, paired end run, 8 bp dual indices) with >30 million reads per sample.Sample Collection - Cell lines were taken from the stock of the cell lines bank (Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures). Cell lines were authenticated by DNA profiling and cytogenetics.Library Construction - Strand-specific (fr-first strand) mRNA-libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Frankfurt am Main, Germany) and amplified.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads were mapped and counted via HTSeq to human Gencode 26. Raw counts per gene and normalised reads via DESeq2 were aggregated and calculated.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensClaudia PommerenkefalseComparative multiparametric evaluation of the suitability of different FBS-free replacement media for widely used human cancer cell linesDespite ethical concerns and scientific drawbacks, fetal bovine serum (FBS) remains a common supplement of culture media for continuous cancer cell lines. FBS alternatives like human platelet lysate (hPL) as well as animal-component free, chemically defined media (CDM) are commercially available for many years. Nevertheless, the acceptance of such alternative media is limited because data verifying the stability of the phenotype and function of a cell line in the alternative media are often lacking. Here, we have adapted four widely used human cancer cell lines (HELA, HL-60, JIMT-1, K-562) to hPL supplemented media and different CDM. To evaluate the suitability of the FBS-free replacements in comparison to the FBS media, we systematically analyzed the different cultures in respect to recovery after cryopreservation, STR-profiles, proliferation, morphology and their transcriptomes. Neither alterations in STR-profiles nor difficulties after cryopreservation were detected. With the exception of K-562, FBS-free cultures showed a reduced proliferation rate and, in some conditions, slight morphological alterations in comparison to FBS cultures. Transcriptome-wide GSEA indicated that culture media affected expression of genes involved in cholesterol homeostasis in all cell lines, and genes involved in epithelial-mesenchymal transition in HELA and JIMT-1. However, their overall phenotypes remained stable. Hematopoietic differentiation markers were among the differentially expressed genes of HL-60 and K-562 cultures, but their main phenotypes remained very similar which was further confirmed by successful induction of differentiation of HL-60 in FBS-free media. In summary, our multiparametric approach delivers validated data supporting the transition to FBS-free media for the analyzed cancer models.2026-03-24T00:00:00Z2026-03-24T10:05:10.921Z2025-11-25T15:45:38.699ZE-MTAB-16289ERP185633EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184