Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention. Consequently, the current DNA storage systems are often not self-contained, implying that they have to resort to external tools for the restoration of the stored DNA data. This may result in high risks in data loss since the required tools might not be available due to the high uncertainty in far future. To address this issue, we propose in this paper a self-contained DNA storage system that can bring self-explanatory to its stored data without relying on any external tool. To this end, we design a specific DNA file format whereby a separate storage scheme is developed to reduce the data redundancy while an effective indexing is designed for random read operations to the stored data file. We verified through experimental data that the proposed self-contained and self-explanatory method can not only get rid of the reliance on external tools for data restoration but also minimise the data redundancy brought about when the amount of data to be stored reaches a certain scale.