Extended Data Fig. 6: Changes of the immune repertoire in inflammatory polyps and low- or high-grade IN samples.
From: Real-time and programmable transcriptome sequencing with PROFIT-seq
a, Expression level of target genes in adaptive sampling runs and unmanipulated controls. The x and y axis represent the expression level of target genes, the dashed lines represent the threshold of five supporting reads in control and adaptive sampling runs, respectively. P < 0.001, Wilcoxon rank sum test. b, Fraction of T cell receptor (TCR) reads identified by TRUST4. Bar colors represent Illumina total RNA-seq (gray), PROFIT-seq without enriching (yellow), and PROFIT-seq enriching target panel (orange), and background colors indicate different clinical stages. Significant difference between PROFIT-seq and control, P = 0.014, Wilcoxon signed rank test. c, Usage of IG heavy chain isotypes in Illumina total RNA-seq of 18 polyp samples. Colors represent different isotypes of IG heavy chains. d, Utilization of 7 IGHV and 6 IGHJ families in PROFIT-seq and Illumina total RNA-seq data. The middle lines represent the median and the lower and upper bounds represent the first and third quartiles. The upper and lower whiskers represent the limits of 1.5 inner quantile ranges, and points outside this range are plotted as outliers. e, Heatmap presentation of VJ combinations in all samples. Colors indicate the relative utilization values normalized across 18 samples. f, Alpha diversity of colorectal polyp microbiome in different stages. g, Schematic view of the PCNP-RPS18 fusion event. The supporting reads are indicated below the gene structure. Source numerical data are available in source data.
