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Series GSE254936 Query DataSets for GSE254936
Status Public on Mar 04, 2024
Title Proteogenomic analysis reveals adaptive strategies to alleviate the consequences of aneuploidy in cancer
Organism Homo sapiens
Experiment type Genome variation profiling by array
Genome variation profiling by genome tiling array
Summary Aneuploidy is prevalent in cancer, conferring fitness advantage, multidrug resistance, and poor prognosis. In contrast, experimentally induced aneuploidy often results in adverse effects and impaired proliferation. This paradox underscores the necessity of cancer cells to adapt to abnormal chromosome numbers. To identify molecular mechanisms of adaptation to aneuploidy, we initiated in vitro evolution of cells with extra chromosomes added via microcell-mediated chromosome transfer. To this end, we cultured cells in a nutrient-rich medium for 50 passages or plated the cells at a low density and selectively collected the largest colonies originating from a single cell (colony selection). The anaylsis of somatic copy number variations in the evolved cell lines was then carried out based on low-coverage whole genome sequencing (WGS) and array-based comparative genomic hybridization (aCGH).
Overall design Detection of copy number variations using genome-wide chromosomal genomic hybridization (CGH) analysis with aneuploid cell lines derived from HCT116 and RPE-1 cell lines before (passsage 0) and after in-vitro evolution (along their near-diploid parental counterparts) and with commercially available gDNAs as references.
Contributor(s) Boekenkamp J, Keuper K, Storchova Z, Stingele S
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Submission date Feb 02, 2024
Last update date Mar 05, 2024
Contact name Jan-Eric Boekenkamp
Organization name University of Kaiserslautern-Landau
Department Molecular Genetics
Street address Paul-Ehrlich-Strasse 24
City Kaiserslautern
ZIP/Postal code 67663
Country Germany
Platforms (2)
GPL5477 Agilent-014950 Human Genome CGH Microarray 4x44K (Feature Number version)
GPL10123 Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version)
Samples (13)
GSM8060410 HCT116_WT_passage0 [HCT116]
GSM8060411 HCT116_WT_colonyselection [Hcs]
GSM8060412 HCT116_trisomy5_passage0 [Htr5]
BioProject PRJNA1072666

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE254936_Matrix-Agilent-014950.txt.gz 2.6 Mb (ftp)(http) TXT
GSE254936_Matrix-Agilent-022060.txt.gz 1.9 Mb (ftp)(http) TXT
GSE254936_RAW.tar 211.8 Mb (http)(custom) TAR (of TXT)

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