Our genomes contain the complete set of information necessary to specify our development from a single totipotent cell to a complex multicellular organism, and in each of these cell types, and their responding states, different sets of genes are expressed through transcription. Determining the transcriptome is thus crucial for understanding cellular identity, gene regulation and human disease.The FANTOM consortium, an international collaboration led by RIKEN, has achieved a number of significant research achievements in the 17 years since its establishment in 2000. Through its examination of various cell types in the human, mouse, rat, dog, chicken, and rhesus monkey, it has made major advances in understanding how our genes are transcribed into RNA and what roles those RNAs play in the body. In particular, research based on the FANTOM atlases led to the realization that so-called “junk RNA,” which is not translated into proteins, is actually important for the expression of the genome. In the past, most publications from FANTOM focused on these research achievements, but now, a team led by scientists from the RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, RIKEN Omics Science Center, RIKEN Advanced Center for Computing and Communication, and Harry Perkins Institute of Medical Research has published new series of articles in Scientific Data focusing on the data resources underlying the atlases, illustrating how it was developed and the analytical methods used. The new articles have been made into the FANTOM5 collection at Nature Publishing Group along with the previously published articles on the consortium’s research achievements. Associated data are openly available with the idea that the FANTOM5 collection will stimulate the re-use of its data, which will contribute to open science in many areas of the life sciences.