RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines

RNA expression levels are partially determined by RNA stabilities. Long-lived RNAs accumulate to higher levels than rapidly degraded RNAs when transcribed at the same rate. The extent to which RNA decay contributes to differences in gene expression between genes in the same cell or between different cell types has not been extensively examined. This is in part because reproducible RNA half-life estimates from different biological contexts have not been broadly collected and curated. To address this, we have developed RNAdecayCafe, a database of high-quality RNA half-life estimates in multiple human cell lines. RNAdecayCafe makes use of pulse-label nucleotide recoding RNA-seq data (namely SLAM-seq and TimeLapse-seq), which we found to provide consistent and orthogonally validated half-life estimates. In total, RNAdecayCafe provides half-life estimates from 11 different human cell lines across 15 datasets and a total of 64 samples that were uniformly processed with a set of optimized bioinformatic tools we recently developed (the EZbakR suite). We showcase how this resource reveals the previously underappreciated role of RNA stability in shaping gene expression. RNAdecayCafe will provide a robust database for future studies of RNA decay.