REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
All raw and processed data	This paper	https://doi.org/10.22002/hf6zq-zmg82
Forelimb mouse atlas	He et al.28	ENCODE: ENCSR713GIS
Early gastrulation mouse atlas	Pijuan-Sala et al.29	https://github.com/MarioniLab/EmbryoTimecourse2018
Early gastrulation mouse atlas (endoderm)	Nowotschin et al.30	https://endoderm-explorer.com/
Epithelial/mesenchymal transition atlas	Dong et al.31	GEO: GSE87038
Mammalian embryogenesis atlas	Chang et al.27	GEO: GSE122187
Tabula Muris and Tabula Muris Senis	Tabula Muris Consortium25,26	tabula-muris-senis.ds.czbiohub.org
Software and algorithms
Code for all analyses and figures generated in this paper	This paper	Release version: https://doi.org/10.22002/37gwp-bjg24 and Development version: https://github.com/labowitz/motifs
Scanpy	Wolf et al.68	https://scanpy.readthedocs.io/en/stable/
Motif finder	This study	https://github.com/labowitz/motifs
PathBank	Wishart et al.40	https://www.pathbank.org/