Project description:This dataset consists of single-nucleus RNA-seq and single-cell ATAC-seq (10X multiome) data from 3 embryonic stages (E14.5-16.5) of pancreatic epithelial cells from Neurogenin3 (Ngn3)-Venus fusion (NVF) homozygous mice. Endocrine progenitor cells (NVF+) were enriched by FACS cell sorting.
Project description:Tissue repair responses in metazoans are highly coordinated by different cell types over space and time. However, comprehensive single-cell based characterization covering this coordination is lacking. Here, we captured transcriptional states of single cells over space and time during skin wound closure, revealing choreographed gene expression profiles. We identified shared and prominent space-time patterns of cellular and gene expression enrichment: which we call multicellular ‘movements’ and which spanned multiple cell types. We validated some of the discovered space-time movements using large volume imaging of cleared wounds and demonstrated the value of this analysis to predict gene products made by macrophages or fibroblasts, which activated gene programs in the opposite cell type. Finally, using two different tumor models, we tested the hypothesis that tumors are like ‘wounds that never heal’ finding conserved wound healing movements in the tumor space, wherein some movements were preferentially used in one tumor versus another.
Project description:We molecularly characterized thousands of liver hepatocytes cells at different time points around the circadian clock. This enable us to reconstruct mRNA expression profiles in space and time.
Project description:The discovery of highly enantioselective catalysts and elucidating their generality face great challenges due to the complex multidimensional chemical space of asymmetric catalysis and inefficient screening methods. Here, we develop a general strategy for ultra-high-throughput mapping the chemical space of asymmetric catalysis by escaping the time-consuming chiral chromatography separation. The ultrafast (~1000 reactions/day) and accurate (median error < ±1%) analysis of enantiomeric excess are achieved through the ion mobility-mass spectrometry combines with the diastereoisomerization strategy. A workflow for accelerated asymmetric reaction screening is established and verified by mapping the large-scale chemical space of more than 1600 reactions of α-asymmetric alkylation of aldehyde with organocatalysis and photocatalysis. Importantly, a class of high-enantioselectivity primary amine organocatalysts of 1,2-diphenylethane-1,2-diamine-based sulfonamides is discovered by the accelerated screening, and the mechanism for high-selectivity is demonstrated by computational chemistry. This study provides a practical and robust solution for large-scale screening and discovery of asymmetric reactions.
Project description:This study generated multiome profiling of scRNA-seq and scATAC-seq data from ∼11,000 differentiating mouse embryonic stem cells over a time course. It demonstrates scTIE achieves effective data integration while preserving more biological signals than existing integration methods.
Project description:Space-time Mapping Identifies Concerted Multicellular Patterns and Gene Programs in Healing Wounds and their Conservation in Cancers.