GREIN studies
Gene-level raw counts and study metadata are collected by GEO accession.
A continuously updated transcriptomic resource
Explore endothelial identity across tissues and studies.
Curated mouse and human bulk RNA-seq, together with human single-cell and single-nucleus references, connect broad expression patterns with the diversity of vascular cell types. Explore gene expression, tissue-specific programs, and evidence from published studies through complementary atlases.
Mouse RNA-seq Atlas Snapshot
Updated —
—curated controls
—contributing studies
—shared genes
—tissues
Human RNA-seq Atlas Snapshot
Updated —
—curated controls
—contributing studies
—shared genes
—tissues
Human sc/snRNA-seq Atlas Snapshot
Updated —
—curated controls (cells)
—contributing studies
—gene labels across studies
—tissues
Why endothelial cells?
Gateways to tissues. At the heart of health and disease.
Endothelial cells line our blood vessels, forming the living interface between circulation and tissue. They regulate what passes across that boundary—from oxygen and nutrients to immune cells—and respond to the needs of the organs they serve. Their identity reflects both a shared vascular role and the distinct demands of each tissue.
In disease, this interface can change. Endothelial cells can reinforce or compromise barriers, shape inflammation, and influence tissue repair. Exploring their gene expression across tissues and studies helps reveal what makes each vascular environment distinct—and how those differences may contribute to health and disease.
From public data to explorable evidence
A reproducible pipeline for bulk RNA-seq.
From GREIN to the EC Atlas, approved bulk studies become curated expression profiles, plots, and EC-enriched gene results. Mouse and human atlases retain independent calculations and releases.
Manual curation
Controls, biological replicates, cell identities, tissue, age, sex, and methods are audited.
Standardized atlas build
GREIN-processed gene-level counts retain their study identity, receive common identifiers and curated metadata, and are assembled for atlas-wide normalization and analysis. No batch-effect harmonization is applied.
Mouse and human EC atlases
Plots, PCA and UMAP views, reference scores, EC-enriched gene results, and downloads regenerate automatically.
From published references to cellular detail
A reproducible pipeline for sc/snRNA-seq.
From CELLxGENE and author repositories to the EC Atlas, published references become reviewed endothelial cohorts across tissues. Cell selection, consistent groupings, and documented sources support exploration in a release that updates independently.
CELLxGENE + author repositories
Expression matrices, cell annotations, and tissue metadata come from published human vascular and tissue atlases. The original study, distributing atlas or repository, and source version are recorded.
Defined endothelial cohorts
Author or curated reference annotations identify candidate endothelial cells; study-specific review defines the retained cohorts. Reference criteria, tissue assignments, overlapping cohorts, and unresolved annotations are documented by study.
Validated reference release
Cell identities and tissue labels are mapped for comparison while source annotations remain available. This release uses counts normalized per 10,000; expression processing and published or explicitly recomputed UMAPs retain their study context.
All tissues and Brain
Explore gene expression, vascular cell identities, tissue filters, and study summaries. Download UMAPs and bar graphs as PNG or SVG figures. Cells and nuclei retain their distinct measurement context.
Defined cohorts
Clear biological context
Every atlas makes its selection criteria explicit. Bulk calculations use manually approved controls; sc/snRNA-seq uses source-defined reference cohorts. Clinical context and study-specific limitations remain documented so reference samples are not automatically treated as healthy controls.
Traceable
Studies stay visible
Across all atlases, study labels, tissue and cell identities, and source credits connect expression patterns to their original study and distributing repository. Bulk samples, cells, and nuclei retain their measurement context.
Continuously updated
Independent releases, current views
Each atlas has its own update date for new data or recomputed analyses. Mouse RNA-seq, human RNA-seq, and human sc/snRNA-seq releases update independently; website styling changes do not reset these dates.
Why bulk RNA-seq?
Deep, interpretable profiles from defined cell populations.
Bulk RNA-seq provides strong gene-level coverage and stable expression estimates when the input population has been carefully isolated and annotated. That makes it especially useful for comparing endothelial programs across independent studies and for examining genes that may be difficult to measure consistently in sparse single-cell data.
The atlas does not treat every bulk sample as perfectly pure. Instead, it retains sample provenance, displays individual replicates, and uses reference-cell transcriptomes to evaluate endothelial identity and tissue context.
Why sc/snRNA-seq?
Resolve the cell identities behind the expression.
Single-cell and single-nucleus RNA-seq offer a closer view of the diversity within endothelial populations across tissues. These references let us explore vascular subtypes, examine where candidate markers are expressed, and interpret the signals observed in bulk RNA-seq profiles.
The human sc/snRNA-seq atlas complements the bulk atlas with curated cell identities and tissue and study provenance. Comparisons retain their measurement context so shared expression patterns can be explored without treating cells, nuclei, and bulk samples as interchangeable observations.
Authors of contributing studies
Help us represent your study accurately.
Future development
Where the atlas is going next.
The current control atlas is the foundation. New modules will be added only as suitable datasets are reviewed and harmonized.
Endothelial disease states
Focused comparisons of how endothelial programs change in injury, inflammation, infection, and disease.
More organs
Broader endothelial and tissue-matched reference coverage across additional vascular beds.
Human RNA-seq
Expand the separately harmonized human atlas with additional tissues, reference populations, and disease cohorts.
Collaborations
Have a dataset you would like to compare with the atlas? We welcome collaborations to explore endothelial identity across tissues, experimental conditions, and disease.
Discuss a collaboration →