Extended Data Fig. 3: Consistency of enriched/selective ALEs between FACS-seq and NYGC datasets.
From: TDP-43 loss induces cryptic polyadenylation in ALS/FTD
A). Overlap between ALEs passing enrichment threshold in the ‘Liu’ FACS-seq data34 (Fig. 2a) and splice junctions of ALEs passing selective detection thresholds in the New York Genome Centre (NYGC) ALS Consortium dataset (Fig. 2b). Cryptic ALEs in each intersection group are labelled directly underneath the event count. B). Heatmap of PAS usage in post-mortem FACS-seq data34 for NYGC-specific ALEs. Cells are labelled with and coloured in proportion to the magnitude of the sample-wise difference in PAS usage between TDP-43 depleted (TDPnegative) and TDP-43 positive (TDPpositive) nuclei. Rows are arranged in descending order of the median sample-wise difference in usage (TDPnegative - TDPpositive). Columns represent individual patients within the cohort. C). Detection statistics for FACS-seq specific ALEs in the NYGC ALS Consortium. ALEs are sorted in descending order of the detection enrichment ratio and bars are coloured according to expected presence (gold, ‘True’) or absence (grey, ‘False’) of TDP-43 proteinopathy. ALEs are considered detected if at least 2 junction reads were present in a sample.
