DEE2 2025 updates: growth and development
DEE2 is a database service I co-founded in 2015 aiming to provide uniformly processed gene expression profiles for each and every RNA-seq dataset in NCBI's Sequence Read Archive. After some major revisions, we published the database/service journal article in 2019. Over time, DEE2 has grown dramatically, with the number of datasets and total number of counted reads, as seen in the tables below. Here, I'll walk you through the growth of the database over time and the new features we've added. Growth of DEE2 DEE2 continues to ingest new metadata from NCBI SRA and GEO, and the growth of this metadata set has caused us a lot of issues over time. In the early years of DEE2 we used SRAdb, and then it became too large for its design, so we sought different solutions. Currently we are using pySRA and only fetching quarterly. The size of each request has been a challenge, with human and mouse requests of annual dumps exceeding the 64 GB RAM of our backend workstation! S...