How can I access and analyze a publicly available RNA-seq database?

Some main databases one can use include Gene Expression Omnibus (GEO), European Nucleotide Archive, and EMBL Expression Atlas. The GEO is a broad database which has data generated across various platforms (e.g. microarray, scRNA-seq, bulk RNA-seq). GEO has an in-depth advanced search function to help specify which datasets one wants to find. One can search for a specific organism, study author, or number of samples. To use the European Nucleotide Archive, one can use their advanced search function. Sequence data displayed by ENA can then be downloaded from their FTP servers. EMBL Expression Atlas has explorable and downloadable RNA-seq databases from many organisms, diseases, and tissues. Datasets can be further categorized as “baseline” or “differential” studies to give a better understanding of what is being studied. When datasets are categorized by baseline, it assesses gene expression in different tissues at a steady state. On the other hand, when datasets are categorized differentially, it gives a comparison between two or more conditions.