Merge pull request #19 from rnabioco/resub

Resub
rnabioco · Feb 18, 2021 · 474d43c · 474d43c
2 parents dedc8c3 + ea398e8
commit 474d43c
Show file tree

Hide file tree

Showing 184 changed files with 2,985 additions and 156,299 deletions.
diff --git a/README.md b/README.md
@@ -1,4 +1,8 @@
-## Molecular Tracking Devices to follow molecular dissemination in vivo
+## Molecular Tracking Devices to follow molecular dissemination *in vivo
+
+Shannon M. Walsh\*, Ryan M. Sheridan\*, Erin D. Lucas\*, Thu A. Doan, Brian C. Ware, Johnathon Schafer, Rui Fu, Matthew A. Burchill, Jay R. Hesselberth, and Beth A. Jirón Tamburini
+
+The detection of foreign antigens in vivo has relied on fluorescent conjugation or indirect read-outs such as antigen presentation. In our studies, we found that these widely used techniques had several technical limitations thathave precluded a complete picture of antigen trafficking or retention across lymph nodecell types. To address these limitations, we developed a “molecular tracking device” to follow the distribution, acquisition, and retention of antigen in the lymph node. Utilizingan antigen conjugated to a nuclease-resistant DNA tag, acting as a combined antigen-adjuvant conjugate, and single-cell mRNA sequencing we quantified antigen abundance in lymph node. Variable antigen levels enabled the identification of caveolar endocytosis as a mechanism of antigen acquisition or retention in lymphatic endothelial cells. Thus, these molecular tracking devices enable new approaches to study dynamic tissue dissemination of antigen-adjuvant conjugates and identify new mechanisms of antigen acquisition and retention at cellular resolution in vivo.
 
 ### Data availability
 

diff --git a/docs/LEC_vaccinia_reanalysis.Rmd b/docs/LEC_vaccinia_reanalysis.Rmd
diff --git a/docs/plots/d14/DC_celltype2_d14.pdf b/docs/plots/d14/DC_celltype2_d14.pdf
diff --git a/docs/plots/d14/DC_celltype_d14.pdf b/docs/plots/d14/DC_celltype_d14.pdf
diff --git a/docs/plots/d14/DC_clusters_d14.pdf b/docs/plots/d14/DC_clusters_d14.pdf
diff --git a/docs/plots/d14/DC_gex2_d14.pdf b/docs/plots/d14/DC_gex2_d14.pdf
diff --git a/docs/plots/d14/DC_gex_d14.pdf b/docs/plots/d14/DC_gex_d14.pdf
diff --git a/docs/plots/d14/FRC_celltype_d14.pdf b/docs/plots/d14/FRC_celltype_d14.pdf
diff --git a/docs/plots/d14/FRC_clusters_d14.pdf b/docs/plots/d14/FRC_clusters_d14.pdf
diff --git a/docs/plots/d14/FRC_gex_d14.pdf b/docs/plots/d14/FRC_gex_d14.pdf
diff --git a/docs/plots/d14/LEC_celltype2_d14.pdf b/docs/plots/d14/LEC_celltype2_d14.pdf
diff --git a/docs/plots/d14/LEC_celltype_d14.pdf b/docs/plots/d14/LEC_celltype_d14.pdf
diff --git a/docs/plots/d14/LEC_cluster_celltype_d14.pdf b/docs/plots/d14/LEC_cluster_celltype_d14.pdf
diff --git a/docs/plots/d14/LEC_clusters_d14.pdf b/docs/plots/d14/LEC_clusters_d14.pdf
diff --git a/docs/plots/d14/LEC_gex2_d14.pdf b/docs/plots/d14/LEC_gex2_d14.pdf
diff --git a/docs/plots/d14/LEC_gex_d14.pdf b/docs/plots/d14/LEC_gex_d14.pdf
diff --git a/docs/plots/d14/celltype2_d14.pdf b/docs/plots/d14/celltype2_d14.pdf
diff --git a/docs/plots/d14/cluster_celltype1_d14.pdf b/docs/plots/d14/cluster_celltype1_d14.pdf
diff --git a/docs/plots/d14/cluster_umap_d14.pdf b/docs/plots/d14/cluster_umap_d14.pdf
diff --git a/docs/plots/d14/d14_BEC_markers.csv b/docs/plots/d14/d14_BEC_markers.csv
diff --git a/docs/plots/d14/d14_DC_markers.csv b/docs/plots/d14/d14_DC_markers.csv
diff --git a/docs/plots/d14/d14_FRC_markers.csv b/docs/plots/d14/d14_FRC_markers.csv
diff --git a/docs/plots/d14/d14_FRCcd34pos_markers.csv b/docs/plots/d14/d14_FRCcd34pos_markers.csv
diff --git a/docs/plots/d14/d14_LEC_markers.csv b/docs/plots/d14/d14_LEC_markers.csv
diff --git a/docs/plots/d14/d14_LECsub_markers.csv b/docs/plots/d14/d14_LECsub_markers.csv
diff --git a/docs/plots/d14/d14_Nr4a1SC_markers.csv b/docs/plots/d14/d14_Nr4a1SC_markers.csv
diff --git a/docs/plots/d14/d14_cDC1_markers.csv b/docs/plots/d14/d14_cDC1_markers.csv
diff --git a/docs/plots/d14/d14_cDC2tbetneg_markers.csv b/docs/plots/d14/d14_cDC2tbetneg_markers.csv
diff --git a/docs/plots/d14/d14_cLEC_markers.csv b/docs/plots/d14/d14_cLEC_markers.csv
diff --git a/docs/plots/d14/d14_combined.pdf b/docs/plots/d14/d14_combined.pdf
diff --git a/docs/plots/d14/d14_corr_DC.csv b/docs/plots/d14/d14_corr_DC.csv
diff --git a/docs/plots/d14/d14_corr_LEC.csv b/docs/plots/d14/d14_corr_LEC.csv
diff --git a/docs/plots/d14/d14_corr_immgen.csv b/docs/plots/d14/d14_corr_immgen.csv
diff --git a/docs/plots/d14/d14_corr_migDC.csv b/docs/plots/d14/d14_corr_migDC.csv
diff --git a/docs/plots/d14/d14_corr_tabmuris.csv b/docs/plots/d14/d14_corr_tabmuris.csv