Mus musculus Raw sequence reads. Mus musculus

To examine whether USP7 regulates CSR through DDR and DSB repair, we examined the pattern of Su-Sa junctions by high-throughput genome-wide translocation sequencing (HTGTS) in CI/CIT-stimulated WT and USP7 deficient cells. A single bait primer annealing to the very 5' Su region was used to linearly-amplify the Su-Sx junctional sequences followed by ligation to a partial duplex DNA linker that were synthesized to contain six random nucleotides at the 3' end of the longer oligo to allow base-pairing with the linearly-amplified random Su-Sx sequences. Addition of Illumina sequencing adaptors at the 5'Su and the linker sides by two more rounds of PCR will generate libraries for 2nd-generation sequencing to reveal the Su-Sx junctional sequences. Depending on which end of the downstream Sx DSB is joined to the donor Su break end, Su-Sa junctions can be classified into deletional and inversional joins. A deletion joining removes the sequences in between the Su and Sa regions, whereas an inversion event generates a ligation product that contains the internal Su-Sa sequences inverted so that neither IgM nor IgA antibody could be possibly produced. In addition, there are cases where junctions are mapped to regions outside of the core Sa either in the deletion orientation downstream to Sa, or in the inversional orientation upstream to Sa. As AID-dependent DSBs are nearly exclusively generated in the core Sa, there junctions have to be formed by joining of Su bait breaks to resected Sa DSB ends in either direction, they are thus designated as resection joins.