A lymphatic-stem cell interactome regulates intestinal stem cell activity

UID: 11340

Author(s): Niec, Rachel E.*, Chu, Tin Yi*, Gur-Cohen, Shiri, Schernthanner, Marina, Pe'er, Dana*, Fuchs, Elaine * MSK affiliated

Description: Summary from GEO:

"Single-cell RNA-sequencing of murine small intestinal organoid cultured with and without lymphatic endothelial cells:
Purpose: To identify differences in cell composition in murine organoids upon coculture with lymphatic endothelial cells
Results: We recovered 818 cells with a median of 37750 UMIs per cell for the organoid alone and 1233 cells with a median of 79354 UMIs per cells for the cocultured organoid condition.
Conclusions: scRNASeq reveals different cell composition in organoids cocultured with lymphatic endothelial cells compared to control

Single-cell RNA-Sequencing of murine small and large intestinal tissue:
Purpose: To generate a reference dataset of all major cell types present in the small and large intestine of the mouse
Results: For the small intestine we recovered 8842 cells with a median of 4088 UMIs per cell compared to 8646 cells with a median of 10009 UMIs per cell for the large intestine.
Conclusions: scRNASeq recovers all of the major epithelial, immune and stromal cell types in the intestine.

Spatial transcriptomic profiling of murine small and large intestine:
Purpose: To spatially map the major cell types in the mouse intestine and infer cell:cell communication from neighboring cells
Conclusions: Spatial transcriptomic profiling of the mouse small and large intestine reveals all major cell types and allows for cell:cell signaling analyses upon integration with our matching scRNA-Seq data"

Subject of Study

Subject(s)

Access via GEO

Accession #: GSE190037

Access via BioProject

Accession #: PRJNA785618

Access via SRA

Accession #: SRP348949
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, BioProject, and SRA databases provides open access to these files.
Associated Publications: Niec R, Chu T, Schernthanner M, Gur-Cohen S, Hidalgo L, Pasolli H, Luckett K, Wang Z, Bhalla S, Cambuli F, Kataru R, Ganesh K, Mehrara B, Pe'er D, Fuchs E. Lymphatics act as a signaling hub to regulate intestinal stem cell activity. Cell Stem Cell. 2022; 29(7):1067-1082.e18.
Equipment Used: Illumina NextSeq 500

Illumina NovaSeq 6000
Dataset Format(s): TSV, TAR, MTX
Dataset Size: 301.1 MB

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