Extended Data Fig. 3: Schematic of LAM-ESC and LAM-recombination methods.

a, LAM-ESC and LAM-recombination are based on LAM-HTGTS that was originally described by Hu et al.³². LAM-ESC and LAM-recombination directly amplify SJ and coding junctions from sonicated genomic DNA using linear amplification-mediated PCR, followed by bead enrichment and on-bead bridge adapter ligation. This enables exponential PCR amplification and labelling of the enriched PCR products with MiSeq (AmpEZ I5 and I7) adapters. Cas9-mediated blocking is introduced to remove germline sequences from amplified LAM-ESC products. The purified Cas9/sgRNA (RNP) complex is targeted by sgRNAs specific to the IGK and IGL loci. b, Schematic of the designed biotinylated oligo, nested primer and a Cas9 targeting site for LAM-ESC for a given J gene segment. The amplified libraries are sequenced via Amplicon sequencing and the reads mapped to the IGL and IGK loci using a custom Python script (https://github.com/Boyes-Lab/LAM-ESC-Recombination)³³. ESCs resulting from inversional recombination events are excluded from our analyses. Likewise, ESCs from intra-KV recombination, between bona fide 12-RSSs and flipped 23-RSSs at a subset of KV gene segments³⁴, are not detected, since LAM-ESC involves amplification from J regions. The specificity of the pipeline was verified via control experiments with HeLa genomic DNA that generated only negligible background reads for LAM-ESC or LAM-recombination.