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Series GSE162645 Query DataSets for GSE162645
Status Public on Jan 27, 2021
Title Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation [aCGH]
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary In this study, we compared the genomic landscape of resistant cell line HaCaT/SM to its progenitor HaCaT in order to gain insights into genetic changes associated with continuous alkylation and oxidative stress. We established chromosome numbers by cytogenetics, analyzed DNA copy number changes by means of array CGH, employed the genome-wide chromosome conformation capture technique Hi-C to detect chromosomal translocations and defined mutational signatures based on whole genome sequencing data. We observed the SM-associated elimination of the initially prevailing hypotetraploid cell population in favor of a hyperdiploid one, which contrasts with previous observations that link polyploidization to increased tolerance and adaptability towards genotoxic stress. Furthermore, we observed an accumulation of chromosomal translocations, frequently flanked by DNA copy number changes, which indicates a high rate of DNA double strand break misrepair. HaCaT/SM-specific single nucleotide variants showed enrichment of C>A and T>A transversions and a lower rate of deaminated cytosines in the CpG dinucleotide context. Given the frequent use of HaCaT in toxicology this study provides a valuable data source with respect to the original genotype of HaCaT and the mutational signatures associated with chronic alkylation and oxidative stress.
 
Overall design Analysis of DNA copy number changes by means of array CGH in the sulfur mustard-resistant cell line HaCaT.
 
Contributor(s) Ullmann R, Kaatsch HL
Citation(s) 33498964
Submission date Dec 04, 2020
Last update date Jan 30, 2021
Contact name Hanns Leonhard Kaatsch
E-mail(s) hannsleonhardkaatsch@bundeswehr.org
Organization name Bundeswehr Institute of Radiobiology
Street address Neuherbergstra├če 11
City Munich
ZIP/Postal code 80937
Country Germany
 
Platforms (1)
GPL9777 Agilent-021850 SurePrint G3 Human CGH Microarray (Feature Number version)
Samples (3)
GSM4956162 HaCaT [aCGH]
GSM4956163 HaCaT_SM [aCGH]
GSM4956164 HaCaT_SM_vs_HaCaT [aCGH]
This SubSeries is part of SuperSeries:
GSE162646 Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation
Relations
BioProject PRJNA682537

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
GSE162645_RAW.tar 131.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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