Cell Reports · 2022 · 47 citations · 48 references
Life SciencesDevelopmental BiologyMolecular BiologyEmbryogenesisOrganogenesisTranscriptomicsDigestive System DevelopmentEpithelial DifferentiationEpithelial MorphogenesisEpithelial-mesenchymal InteractionsIntestinal DevelopmentMesenchymal-epithelial InteractionsCell Fate DecisionsDigestive DevelopmentEmbryology Of The Digestive SystemGut RegionalizationIntestinal MorphogenesisOrganoidsRna Sequencing (Rna-seq)Single-cell Rna Sequencing
large-intestinal mesenchyme. The regionalization and heterogeneity of both the epithelium and the mesenchyme can be traced back to E9.5. The spatiotemporal distributions of cell clusters and the mesenchymal-epithelial interaction analysis indicate that a coordinated development of the epithelium and mesenchyme contribute to the stomach regionalization, intestine segmentation, and villus formation. Using the gut tube-derived organoids, we find that the cell fate of the foregut and hindgut can be switched by the regional niche factors, including fibroblast growth factors (FGFs) and retinoic acid (RA). This work lays a foundation for further dissection of the mechanisms governing this process.
48
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 56.2K citations · Full text
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Guangchuang Yu, Li-Gen Wang, Yanyan Han et al. · OMICS A Journal of Integrative Biology · 2012 · 38.3K citations
Comprehensive Integration of Single-Cell Data
Tim Stuart, Andrew Butler, Paul Hoffman et al. · Cell · 2019 · 16.9K citations · Full text
Inference and analysis of cell-cell communication using CellChat
Suoqin Jin, Christian F. Guerrero‐Juarez, Lihua Zhang et al. · Nature Communications · 2021 · 8.3K citations · Full text