mutREAD sequencing data from ""Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity""

Monoclonal RKO - DOX -Cas9 -P2A - GFP cell lines that also have a homozygous knock -out of UNG2 - / - and either nothing or MYC -mCherry -P2A -3xHA -A3H -I over -expressed were generated. As a control the cell line without A3H -I over -expression was transduced with sgA3B to generate A3B knock -out cells. These cells were transduced with DualCRISPR -hU6 -sgRNA -mU6 -sgRNA - iRFP670 targeting indicated genes and bulk sorted for iRFP + cells. Cas9 was induced with DOX and sequential samples collected up to 10 days after induction. Cells were harvested on Day 6 and Day 10 after Cas9 induction. E3 ligase knock -outs were verified by WB and gDNA extracted. This dataset contains the reads of three clonal cell lines denoted RA1, R2, and R2+219. These were derived from the parental clone (RKO - DOX -Cas9 -P2A - GFP cell lines that also have a homozygous knock -out of UNG2 - / - ).Three E3-ligases (sgHUWE1, sgUBR4, and sgUBR5 ) were knocked out to test the effect of knockout versus the control genotype (sgAAVS1) on the generation of apobec related mutational signatures SBS2 and SBS13.The genetic background of the clonal cell lines is as follows:RA1 = [UNG -/-, A3H-I overexpression]R2 = [UNG -/-]R2+219 = [UNG -/-, sgA3B (knockout)] Raw reads were processed according to GATK4 best practices. Briefly, reads were mapped to the GRCh38 human reference genome and single nucleotide substitutions and InDels were called with Mutect2 in tumor-only mode. Resulting variants were filtered by only retaining variants with Mutect2 quality status ‘PASS’ and variant allele frequency (VAF) between 0.3 and 0.7. Variants In order to exclude cell-line specific variants found in the parental clone, we obtained 30x whole genome sequencing (BGITech Global, BGI Genomics Co., Ltd.) from the parental clone (RKO-DOX-Cas9-P2A-GFP) and retained only variants which were not also present in the parental clone.