Omics · study · 2026
Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment
Listed in NCBI GEO
We used single-cell RNA sequencing to interrogate granulomas from Mycobacterium marinum infected zebrafish (Danio rerio) of a genetic mutant.
Description
This sample was compared to a previously published granuloma scRNAseq dataset from wildtype zebrafish. Granulomas are comprised of several cell types and we sought to understand the consequences of genetic disruption of the gene leukotriene A4 hydrolase (lta4h) on granuloma cells types and cell-specific transcription.
This is the first comparison of mycobacterial granuloma scRNAseq from a genetic mutant to wildtype.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE299nnn/GSE299987 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299987 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1277811 ncbi.nlm.nih.gov/bioproject/PRJNA1277811 ↗
project · from NCBI GEO
Topics
- Stated by source
- Danio rerio · Expression profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 75%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE299987 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:7955 | 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 |