Skip to main content
. 2023 Aug 28;6(11):e202301959. doi: 10.26508/lsa.202301959

Figure 1. Sample diversity analysis.

Figure 1.

(A) Experimental framework combining laser capture microdissection (LCM) and Rep-seq from human lymph node (LN) GC’s genomic DNA to analyze F (functional) and NF (non-functional) rearrangements via semi-nested PCR amplifying the leader (LD) and framework region 1. Details of the experimental approach are provided in the methods section. The area within the dashed lines corresponds to the area that was isolated by LCM and used for genomic DNA extraction. (B) H&E staining performed in parallel with LCM is shown (10X magnification) (B) Sørensen–Dice similarity between each sample in terms of clonal abundance. (C) Clone abundance across samples, denoted as Vgene_JunctionLength_Jgene (only the 20 most abundant clones are shown in the legend for visual clarity). (D) Proportion of sequences belonging to the dominant clone, expanded clones, and non-expanded clones in each sample. (E) Number of sequencing reads in each sample (in units of 1,000). (F) Diversity analysis across samples in terms of dominance, richness, Shannon entropy, and evenness, where q D corresponds to Hill’s unified notation. To highlight the relevance of studying GCs individually, each sample (blue) is compared with an artificial sample of equivalent size sub-sampled from combining all the obtained sequences (grey).