The paper uses spatial transcriptomics to identify injury-specific microenvironments and molecular interactions in the mouse kidney during injury and regeneration.

bioRxiv · Nov 22, 2023 · PreprintMolecular Biology

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Peng He, Brian A. Williams, Diane E. Trout, Georgi K. Marinov, Henry Amrhein, Libera Berghella, Say-Tar Goh, Ingrid Plajzer-Frick, Veena Afzal, Len A. Pennacchio, Diane E. Dickel, Axel Visel, Bing Ren, Ross C. Hardison, Yu Zhang, Barbara J. Wold

The paper quantifies the mouse embryo transcriptome from E10.5 to birth using whole-tissue and single-cell RNA-seq, identifying key gene expression patterns and cell types.

Nature · Jul 29, 2020Peer-reviewedDevelopmental Biology

Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus

Yupeng He, Manoj Hariharan, David U. Gorkin, Diane E. Dickel, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Ah Young Lee, Yuan Zhao, Hui Huang, Brian A. Williams, Diane E. Trout, Henry Amrhein, Rongxin Fang, Huaming Chen, , Joseph R. Ecker

The paper maps DNA methylation changes across 12 mouse tissues at 8 developmental stages, identifying methylation variant regions and tissue-specific enhancers linked to human genetic diseases.

Nature · Jul 29, 2020Peer-reviewedGenomics

Systematic mapping of chromatin state landscapes during mouse development

David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, Joshua Chiou, André Wildberg, Bo Ding, Bo Zhang, Mengchi Wang, J. Seth Strattan, Jean M. Davidson, Yunjiang Qiu, , Bing Ren

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

Nature · Jul 29, 2020Peer-reviewedGenomics