We collected 44 stage II to IV melanoma and paired adjacent normal tissues from Fudan University Shanghai Cancer Centre and Xiangya Hospital between May 2018 and September 2020. The median age of the melanoma patients was 62.5 years (range, 11 to 85 years), with 13(30%) male patients and 31 (70%) female patients.
Steps to reproduce
All RNA-seq data were aligned to the reference genome hg19 using the HISAT2 with the default setting. Stringtie was used to calculate the transcriptional expression level as FPKM. To characterize the dynamic APA events for RNA-seq data, we obtained the genomic coordinates of RNA transcripts (hg19) for APA events calling from USCS genome browser (http://genome.ucsc.edu) and utilized the well-established algorithm DaPars(8) (https://github.com/ZhengXia/DaPars) to identify the alternative proximal polyA site and calculate the Percentage of Distal polyA site Usage Index (PDUI) for each transcript.