Characterizing the transposome and its activity Sequencing technologies enabled us to decode sequence of bases that shape the genome and to identify sequence stretches with biological functions such as genes. Such technologies also enable us to study the expression and regulation base sequences. Intriguingly transposable elements (TEs) can occupy a substantial proportion of a genome. However quantification of TE expression remains challenging due to their high sequence similarity and the limited lengths of base sequences decoded by state of the art sequencing technologies. I evaluated five TE quantification software applications with respect to their performance in quantifying the expression of individual TEs. My tool evaluation was based on simulated datasets created using publicly available as well as self implemented simulation software. I showed that modified SalmonTE can be applied for reliable differential expression analyses in model and non model organisms. Consequently I applied modified SalmonTE to study (differentially) TE expression in blood brain and skin of mice of different ages (6 and 24 months). While previous family level studies of TE expression identified up regulation of TEs as a characteristic of aging my results indicate that individual TEs are also commonly down regulated during aging. Integration of transcription start site sequencing data identified TEs with their own promoters revealing that these elements can be regulated by transcription factors of the Sox family. Co regulation of TEs and host genes indicates potential biological functions of independently expressed TEs. Together this study revealed the expression dynamics of individual TEs during aging and provides a comprehensive resource of independently expressed TEs. These data can be a promising starting point to intensify research into locus specific TE expression to gain a better understanding of the biological functions interactions and regulation of TEs.