The introduction and constant improvement of RNA-sequencing technologies has enabled us to interrogate the human transcriptome at nucleotide resolution, revealing distinct RNA biotypes beyond protein-coding RNAs. Several consortium-based efforts have contributed to the discovery and quantification of these RNA biotypes in heterogeneous sample collections. However, these studies have mostly applied RNA-sequencing technologies dedicated to the small RNA and polyadenylated RNA fraction of the transcriptome. As a result, we still lack a systematic survey of the non-polyadenylated transcriptome and the circularized transcriptome and their relationship to other RNA biotypes. During my PhD research, I contributed to the generation of a more comprehensive atlas of the human transcriptome through the integration of matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human samples including 45 tissues, 162 cell types and 93 cell lines. The generated transcriptome constitutes a unique resource to further explore RNA biology, function and relation to disease and represents a substantial expansion of the current catalogue of human ncRNAs (including lincRNAs, asRNAs, circRNAs, and miRNAs) and their regulatory interactions across a large set of cell types, tissues and cancer cell lines.