Imaging · study · 2026
High-resolution spatial transcriptomics of human liver with VisiumHD
Listed in NCBI GEO
The liver plays a critical role in metabolism and immune function.
Description
These crucial functions are diminished in chronic liver diseases, leading to over two million deaths annually worldwide due to liver failure. Single-cell transcriptomics has provided insights into the cellular composition of the liver in health and disease, but is inherently biased due to cell type-specific enrichment and destruction during the single-cell dissociation process.
Previous work has highlighted difficulties in capturing specific populations such as cholangiocytes and hepatocytes. Spatial transcriptomics is a promising approach that does not have inherent bias for cell populations and adds important spatial context. Until recently, spatial transcriptomics technologies have only been at a multi-cellular resolution leading to mixed signals from different cell types.
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The latest spatial transcriptomic technology from 10X Genomics, VisiumHD, enables high-resolution spatial mapping of gene expression in tissue samples, offering a sophisticated platform for exploring the cellular composition of the liver. With a bin width of 2um, it can quantify transcripts at a sub-cellular resolution. Samples from three healthy human liver donors were sequenced and cells were clustered into cell types by integrating spatial transcriptomic data with existing single-cell reference maps.
Spatially distinct cell signatures were identified through differential expression analyses and a high-resolution map of the liver was created. This resource provides cell-level and spatially-resolved insights into the cellular and geographical heterogeneity of the liver to serve as a resource for researchers to identify disease-specific spatial signatures and novel therapeutic targets.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE311nnn/GSE311383 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311383 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1369387 ncbi.nlm.nih.gov/bioproject/PRJNA1369387 ↗
project · from NCBI GEO
- PubMed 42342734 pubmed.ncbi.nlm.nih.gov/42342734 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Homo sapiens · Other
- From keywords
- Life Sciences
- Inferred from text
- Biochemistry and cell biology 70% · Disease 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE311383 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:disease | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].anzsrc:group:3101 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (70%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:other | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |