Droplet-based (10X) scRNAseq was performed on sorted mouse peripheral lymph node (LN) CD45- CD31- stromal cells from uninfected mice (2,571 cells) and mice at day 15 post-infection with LCMV-Armstrong (11,672 cells).
Data from both samples were combined with canonical correlation analysis and similar cells were grouped via unsupervised graph-based clustering. Clusters were named for their defining features and their association with known LN stromal expression.
Differential expression for each cluster available in Tables S2-S8 of our publication.
Rodda LB, Lu E, Bennett ML, Sokol CL, Wang X, Luther SA, Barres BA, Luster AD, Ye CJ and Cyster JG. Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity. Immunity Resource. (Accepted).
GEO Database Accession: GSE112903
Shaurya Dhingra and Lauren B. Rodda
Satija et al., Nature Biotechnology. 2015.
Butler and Satija, biorXiv. 2017.
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