CFM: a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation

Abstract

Cell fate engineering technologies are critically important for basic and applied science, yet many protocols for direct cell conversions are still unstable, have a low yield and require improvement. There is an increasing need for a data aggregator containing a structured collection of protocols - preprocessed, verified, and represented in a standardized manner to facilitate their comparison, and providing a platform for the researchers to evaluate and improve the protocols. We developed CFM (cell fate mastering), a database of experimentally validated protocols for chemical compound-based direct reprogramming and direct cell conversion. The current version of CFM contains 169 distinct protocols, 113 types of cell conversions, and 158 small molecules capable of inducing cell conversion. CFM allows stem cell biologists to compare and choose the best protocol with high efficiency and reliability for their needs. The protocol representation contains PubChem CIDs and Mechanisms Of Action (MOA) for chemicals, protocol duration, media , and yield with a comment on a measurement strategy. Ratings of the protocols and feedback from the community will help to promote high-quality and reproducible protocols. We are committed to a long-term database maintenance strategy. The database is currently available at https://cfm.mipt.ru}{cfm.mipt.ru

DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion

“…For each small molecule, we represented a small molecule-induced transcriptome profile by a feature vector defined as , where p is the number of genes ( p = 978). Of these, 1486 small molecules were registered in KEGG ( Kanehisa et al 2009 ), and 36 small molecules were experimentally confirmed to induce DR ( Sizykh et al 2021 ).…”