Persistent hindrances to data re-use in single-cell genomics

We evaluated the reusability of publicly available single-cell RNA-sequencing studies (scRNA-seq) from the Gene Expression Omnibus, focusing on the prevalent 10x Genomics-based datasets. Through semi-automated and manual curation, we assessed the availability of cell-level expression count matrices and cell-type annotations. Only around 40% of studies provided readily usable processed count data that could be reliably mapped to GEO metadata, and fewer than 10% included author-provided cell-type labels. Although most studies had raw sequencing files available, few could be re-analyzed automatically without reliance on heuristics. Our findings show that existing practices for scRNA-seq data distribution and sharing are insufficient for effective reuse, and highlight the urgent need for repositories to strengthen and enforce submission requirements, particularly for processed data and cell-type annotations.