I have some RNA-seq datasets from human cells and I am interested to see if the expression of transposable elements (TEs) change in different treatments. I found this easy to do with the plant Arabidopsis thaliana as the TAIR10 annotation of the genome has gene types that are TEs. However, such a gene type does not exist in for the human annotations I have seen https://www.gencodegenes.org/gencode_biotypes.html. My understanding is that repeats like TEs are masked in the released human genomes. Especially as so many TEs are so similar to each other, one could not assign RNA or DNA reads to a specific one, so you might need to look at it on the family level.
My question is, how can I get over this issue and look at RNA-seq data for TEs and all other transcript types in human cells? Are there any good studies that do look at expression changes in human cells that I can use to inspire an analysis approach?