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MicroRNAs (miRNAs), among other small non-coding RNAs, shape the transcriptome and control cellular functions. Although single-cell technologies are now available to study myocardial ischemia response, the study of small RNA regulation is limited by depth of expression, capture efficiency and lack of full coverage of transcripts. In addition, the kinetic expression of miRNAs is unknown. Using paired small and total RNA sequencing, we built an expression atlas to study the temporal dynamics of miRNAs and genes in four major heart cell types after AMI. Expression dynamics reveal enriched functions highlighting cell type-specific AMI stress responses. Many deregulated mouse genes after AMI overlap with known human cardiovascular disease genes. The dataset is highly valuable for additional research on small and long non-coding RNAs, such as regulation of RNA variants by splicing or alternative ORFs. 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