a, HTGTS V(D)J-seq analysis with DQ52-RSS-DN bait in D H –J H +/− line. Major junctional outcomes are deletional DQ52-RSS-DN-to-J H joins (77%) and deletional DQ52-RSS-DN joins to cryptic RSSs near the immediately upstream D H 3-2 region (20%), with the latter probably resulting from secondary events on excision circles following primary J H -to-distal D H joins (left; also, see below). b, Southern blot confirmation of J H Δ lines (done once after PCR confirmation). c, Repeats of HTGTS V(D)J-seq experiments shown in Fig. 3a. Each library was normalized to the same number of DQ52-RSS-UP SE junctions. d, Repeats of Fig. 3b HTGTS V(D)J-seq experiments. Each library was normalized to the same number of DQ52-RSS-UP CE junctions captured by the DQ52-RSS-DN bait (see Methods). Note the near abrogation of cryptic deletional joins near D H 3-2 in J H Δ lines, which is consistent with their excision circle origin. Also, unlike the D H –J H +/− line with germline J H s, robust RC downstream cryptic scanning activity is readily detected in the J H Δ lines. e, Repeats of GRO-seq experiments shown in Fig. 3d. Each library was normalized to a coverage of 10 million 100-nt reads for display. f–i, Model of cohesin loop-extrusion-meditated directional RAG scanning from RC DQ52-RSS-UP to upstream regions until reaching IGCR1 loop anchor. j–m, Model of extrusion-meditated directional RAG scanning from RC DQ52-RSS-DN to downstream regions until reaching the 3′ CBEs loop anchor. Transparent yellow rectangles in f, j indicate, respectively, the upstream and downstream RAG scanning regions with DQ52 upstream and downstream RSS joining to cryptic RSSs shown in schematic form. Other schematics are as described in Fig. 1 and Extended Data Fig. 1. The two models are supported by the directional RAG scanning activity in c, d and Fig. 3a, b.