What this page accomplishes
A map into the atlas
Choose the biological tissue first. Each primary tissue workspace follows the same analysis sequence so results remain comparable without losing tissue context.
Mouse RNA-seq Atlas · Overview
Start with the tissue, then follow the evidence.
This atlas harmonizes curated control bulk RNA-seq studies so endothelial identity can be compared across tissues, studies, and matched reference cell types.
Atlas snapshot
Mouse evidence at a glance
Counts reflect the current locally generated atlas release.
—curated samples
—independent studies
—genes
9tissue workspaces
How to interpret it
Three complementary views
PCA and UMAP show sample-level structure. EC-Enriched Genes tests endothelial-versus-reference evidence. Identity & Composition groups reference context with vascular expression programs as supporting atlas information.
Tissue workspaces
Go directly to the biology.
Every link opens the corresponding analysis within that tissue.
BR
Brain
Brain vascular endothelial cells and matched neurovascular reference populations.
ME
Meninges
Dural lymphatic endothelial cells and meningeal stromal and immune references.
EY
Eye/Retina
Retinal endothelial cells alongside neuronal, glial, immune, photoreceptor, and RPE reference populations.
LU
Lung
Pulmonary endothelial populations compared with epithelial, stromal, and immune cells.
LI
Liver
Sinusoidal endothelial cells in the context of hepatocytes, stellate cells, and liver macrophages.
KI
Kidney
Renal endothelial cells alongside tubular, glomerular, and supporting kidney populations.
HE
Heart
Cardiac endothelial cells alongside cardiomyocytes, fibroblasts, macrophages, and B cells.
BO
Bone/Bone Marrow
Bone and marrow endothelial cells alongside stromal, pericyte, hematopoietic stem/progenitor, neutrophil, and B-cell references. Marrow-derived ECs remain distinct.
GI
GI/Associated Tissues
Intestinal populations, gallbladder tuft cells, and peritoneal macrophages. EC-enrichment and identity calculations retain intestinal tissue references.