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Series GSE230579 Query DataSets for GSE230579
Status Public on Jan 26, 2024
Title Single-mitosis dissection of acute and chronic DNA mutagenesis and repair
Organisms Mus musculus; Mus musculus castaneus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary The mammalian genome is constantly exposed to genotoxins that can lead to mutations and ultimately tumorigenesis. Despite cancer being recognized as a genetic disease, much is still unknown regarding tumor induction and evolution of the cancer genome. To study gradual (reactive oxygen species, ROS) and acute (ultraviolet radiation, UV) mutagenic processes both in vitro and then in vivo, we first use microfluidic separation of cells after a single mitosis following pulse mutagenesis. While UV mutations tend to be fixed after one cell cycle and show mirror image mutation patterns between sister cells from a single mitosis, ROS mutations do not. We next show that while both ROS and UV mutation rates are reduced as a function of transcription, only UV has a strand-specific repair signature. Lastly, we resolve pulse induced lesion segregation to single haplotypes by analysing liver tumour genomes from F1 mice treated with N-nitroso-diethylamine (DEN). In summary, we have established highly controlled systems to study 3 distinct forms of mutagenesis at their inception in mammalian cells, providing insights into how these mutations are fixed at the genome scale.
 
Overall design Whole Genome sequencing of the PF1 cell line following UV treatment and seperation of mitotic sisters. Whole genome sequencing of liver tumors from male F1 mice of a Mus castaneus/C3H cross. Ribo-zero bulk RNA and Omni-ATAC samples of the PF1 cell line
 
Contributor(s) Ginno PA, Odom DT, Taylor MS
Citation(s) 38627597
BioProject PRJNA934746
Submission date Apr 25, 2023
Last update date Apr 26, 2024
Contact name Paul Adrian Ginno
E-mail(s) p.ginno@dkfz-heidelberg.de
Phone 00496221423395
Organization name DKFZ
Department B270
Lab Duncan Odom
Street address Im Neunheimer Feld 280
City Heidelberg
State/province Baden-W├╝rttemberg
ZIP/Postal code 69120
Country Germany
 
Platforms (3)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL30172 NextSeq 2000 (Mus musculus)
GPL33115 Illumina NovaSeq 6000 (Mus musculus castaneus)
Samples (32)
GSM7226974 WGSPF1:Negativecontrol,1stpenning a
GSM7226975 WGSPF1:Negativecontrol,1stpenning b
GSM7226976 WGSPF1:Negativecontrol,1stpenning c

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
GSE230579_F1CastB6_mutations.rds.gz 28.4 Mb (ftp)(http) RDS
GSE230579_PF1_ATAC_Peaks.rds.gz 3.8 Mb (ftp)(http) RDS
GSE230579_PF1_RNA_counts.rds.gz 726.4 Kb (ftp)(http) RDS
GSE230579_PF1_SisterMutations.rds.gz 13.6 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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