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Series GSE264509 Query DataSets for GSE264509
Status Public on May 22, 2024
Title Genomic and phenotypic stability of fusion-driven pediatric sarcoma cell lines [array]
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Human cancer cell lines are the mainstay of cancer research. Recent reports showed that highly mutated adult carcinoma cell lines (mainly HeLa and MCF-7) present striking diversity across laboratories and that long-term continuous culturing results in genomic/transcriptomic heterogeneity with strong phenotypical implications. However, to what extent these limitations in terms of reproducibility may be generalized to all cancer cell lines remained unexplored. Here, we hypothesized that oligomutated pediatric sarcoma cell lines mainly driven by a fusion transcription factor, such as Ewing sarcoma (EwS), were genetically and phenotypically more stable than the previously investigated (adult) carcinoma cell lines. A comprehensive molecular and phenotypic characterization of multiple EwS cell line strains, together with a simultaneous analysis during 12 months of continuous cell culture showed that fusion-driven pediatric sarcoma cell line strains are genomically more stable than adult carcinoma strains, display remarkably stable and homogenous transcriptomes, and exhibit uniform and stable drug response. Additionally, the analysis of multiple EwS cell lines subjected to long-term continuous culture revealed that variable degrees of genomic/transcriptomic/phenotypic changes among fusion-driven cell lines, further exemplifying that the potential for reproducibility of in vitro scientific results may be rather understood as a spectrum, even within the same tumor entity.
Overall design Human cell lines were cultured continously over a period of 12 months and subjected to DNA methylation profiling using Illumina EPIC arrays at three different time points (m0=ITP, m6=MTP, m12=FTP)
Contributor(s) Kasan M, Cidre-Aranaz F, Grünewald TG
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Submission date Apr 21, 2024
Last update date May 28, 2024
Contact name Thomas Georg Philipp Grunewald
Phone 0049-6221-423718
Organization name German Cancer Research Center (DKFZ)
Department Division of Translational Pediatric Sarcoma Research
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (62)
GSM8219178 A673 DS_ITP
GSM8219179 A673 DS_ITP_1
GSM8219180 A673/SHCTRL_ITP
BioProject PRJNA1102876

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Supplementary file Size Download File type/resource
GSE264509_20240314_betas_850K_submittedGEO.xlsx 642.5 Mb (ftp)(http) XLSX
GSE264509_RAW.tar 1.0 Gb (http)(custom) TAR (of IDAT)

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