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| 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
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| 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.
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| 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
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| Contributor(s) |
Ginno PA, Odom DT, Taylor MS |
| Citation(s) |
38627597 |
| BioProject |
PRJNA934746 |
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| Submission date |
Apr 25, 2023 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Paul Adrian Ginno |
| E-mail(s) |
p.ginno@dkfz-heidelberg.de
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| Phone |
00496221423395
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| Organization name |
DKFZ
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| Department |
B270
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| Lab |
Duncan Odom
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| Street address |
Im Neunheimer Feld 280
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| City |
Heidelberg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platforms (3) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL30172 |
NextSeq 2000 (Mus musculus) |
| GPL33115 |
Illumina NovaSeq 6000 (Mus musculus castaneus) |
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| Samples (32)
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| GSM7226977 |
WGSPF1:Negativecontrol,2ndpenning a |
| GSM7226978 |
WGSPF1:Negativecontrol,2ndpenning b |
| GSM7226979 |
WGSPF1:Mitoticsister1,cloneA |
| GSM7226980 |
WGSPF1:Mitoticsister1,cloneB |
| GSM7226981 |
WGSPF1:Mitoticsister1,cloneC |
| GSM7226982 |
WGSPF1:Mitoticsister1,cloneD |
| GSM7226983 |
WGSPF1:Mitoticsister1,cloneE |
| GSM7226984 |
WGSPF1:Mitoticsister1,cloneF |
| GSM7226985 |
WGSPF1:Mitoticsister1,cloneG |
| GSM7226986 |
WGSPF1:Mitoticsister2,cloneA |
| GSM7226987 |
WGSPF1:Mitoticsister2,cloneB |
| GSM7226988 |
WGSPF1:Mitoticsister2,cloneC |
| GSM7226989 |
WGSPF1:Mitoticsister2,cloneD |
| GSM7226990 |
WGSPF1:Mitoticsister2,cloneE |
| GSM7226991 |
WGSPF1:Mitoticsister2,cloneF |
| GSM7226992 |
WGSPF1:Mitoticsister2,cloneG |
| GSM7226993 |
ATAC:BulkATAC,PF1linerep1 |
| GSM7226994 |
ATAC:BulkATAC,PF1linerep2 |
| GSM7226995 |
ATAC:BulkATAC,PF1linerep3 |
| GSM7226996 |
RNA:Ribo-zerototalRNA,PF1linerep1 |
| GSM7226997 |
RNA:Ribo-zerototalRNA,PF1linerep2 |
| GSM7226998 |
RNA:Ribo-zerototalRNA,PF1linerep3 |
| GSM7226999 |
WGS:NormalLiver,F1Cast/B6 |
| GSM7227000 |
WGS:LiverTumor,F1Cast/B6,mouseA1 |
| GSM7227001 |
WGS:LiverTumor,F1Cast/B6,mouseA2 |
| GSM7227002 |
WGS:LiverTumor,F1Cast/B6,mouseA3 |
| GSM7227003 |
WGS:LiverTumor,F1Cast/B6,mouseB1 |
| GSM7227004 |
WGS:LiverTumor,F1Cast/B6,mouseB2 |
| GSM7227005 |
WGS:LiverTumor,F1Cast/B6,mouseB3 |
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| 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 Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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