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Transcriptional basis of mouse and human dendritic cell heterogeneity revealed by single-cell profiling

UID: 11178

Author(s): Brown, Chrysothemis C.*, Gudjonson, Herman*, Pritykin, Yury*, Deep, Deeksha*, Lavallée, Vincent-Phillipe*, Mendoza, Alejandra*, Fromme, Rachel M.*, Mazutis, Linas*, Ariyan, Charlotte Eielson*, Leslie, Christina*, Pe'er, Dana*, Rudensky, Alexander Y.* * MSK affiliated

Description
Summary from GEO:

"Dendritic cells (DCs) play a critical role in orchestrating adaptive immune responses due to their unique ability to serve as a principal antigen-presenting cell type capable of initiating T cell responses. Classical dendritic cells have been divided into two subsets, cDC1 and cDC2, based on phenotypic markers and their distinct abilities to prime CD8 and CD4 T cells and direct their differentiation into effectors. Whilst the transcriptional features of the cDC1 subset have been well characterized, the heterogeneity of cDC2 and the development and function of distinct cell types comprising this subset remain poorly understood. Unbiased single-cell RNA sequencing analysis of DCs, combined with genetic reporter expression and fate-mapping revealed two principal cDC2 lineages, their developmental pathways and transcriptional regulators, including the expression of T-bet and RORt, two key transcription factors known to define functional adaptive and innate lymphocyte subsets. The cDC2 lineages were characterized by distinct metabolic and functional programs with phenotypic conservation observed across tissues. Extending the findings in mice to humans revealed conserved characteristics of DC heterogeneity and the presence of the newly defined DC subsets in human autoimmune disease and cancer."

Overall design from GEO:

"Single-cell RNA sequencing was performed on mouse and human splenic dendritic cells. Two samples of mouse dendritic cells were FACS purified based on Tbx21Cre-RFP reporter expression. Single-cell RNA sequencing was also performed on CD45-positive cells in melanoma tumors from two patients."
Subject of Study
Homo sapiens
Mus musculus
Subject(s)
CD4-Positive T-Lymphocytes
CD8-Positive T-Lymphocytes
Dendritic Cells
Melanoma
RNA-Seq
Single-Cell Analysis
OncoTree Cancer Type(s)
Melanoma
Access via GEO


Accession #: GSE137710

Access via BioProject


Accession #: PRJNA566350

Access via SRA


Accession #: SRP222507

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus. BioProject, and SRA databases provide open access to these files.
Associated Publications
Brown C, Gudjonson H, Pritykin Y, Deep D, Lavallée V, Mendoza A, Fromme R, Mazutis L, Ariyan C, Leslie C, Pe'er D, Rudensky A. Transcriptional basis of mouse and human dendritic cell heterogeneity. Cell. 2019; 179(4):846-863.e24.
Equipment Used
Illumina NovaSeq 6000
Dataset Format(s)
TSV, TAR
Dataset Size
141.1 MB
Data Catalog Record Updated
2024-02-27