Transcriptome Profiling and Tissue Specificity

As for gene annotation, quality-trimmed transcriptomic reads from 13 tissues were mapped to the chromosome assembly with HISAT2 v2.2.1 (Kim et al. 2019 (link)) and the resulting SAM files were converted to BAM format using SAMtools v1.10 (Li et al. 2009 (link)). The resulting BAM files and final gene annotation file were used as input into StringTie v2.1.4 (Pertea et al. 2016 (link)) to quantify expression levels and normalize TPM (transcripts per million). The tissue specificity index (τ) of each gene was calculated using the R package tispec v0.99 (Condon 2020 ) and a two-dimensional histogram was used to display the relationship between τ and expression level (TPM). The number of genes expressed in each tissue and different combinations of tissues were displayed in an Upset plot generated with the UpSetR v1.4.0 R package (Conway et al. 2017 (link)).