Single-Cell RNA sequencing of peripheral lymph node stromal cells (CD45- CD31-)

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).

Visualization

Violin plots report the distribution (height of violin) and probability density (width) of gene expression by cluster with the thickest part of the violin indicating the mode for that cluster. Violin plots can be thought of as a sideways histogram and allow users to compare gene expression between clusters without being misled by outliers, which may be highlighted only because the clusters are of different sizes and many cells do not have detectable expression of that gene (common with single-cell RNA sequencing data). Units are log-normalized unique molecular identifier (UMI) counts.

Samples

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.

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).

Raw Data

GEO Database Accession: GSE112903

Cyster Lab

http://cysterlab.ucsf.edu/

Page Authors

Shaurya Dhingra and Lauren B. Rodda

References

Satija et al., Nature Biotechnology. 2015.
Butler and Satija, biorXiv. 2017.

License

This Shiny web app is licensed under the GNU General Public License v3.0.