Omics · study · 2026
Gene expression profiling of catfish after treatment with copper sulfate and exposure to Flavobacterium columnare
Listed in NCBI GEO
Catfish farming remains number one among U.S. aquaculture production.
Description
Flavobacterium columnare, the causative agent of columnaris disease, produces substantial mortality during the production of freshwater farmed finfish species. F. columnare is ubiquitous in the aquatic environment, and outbreaks of disease are often triggered during the spring and summer months of the catfish production cycle.
As food fish production continues to increase, the frequency of columnaris disease will only continue to rise within the aquaculture industry and thus new preventative measures will be required. Copper sulfate is the most common algaecide used in aquaculture. Copper sulfate has also been suggested as a therapeutant for columnaris disease, as we have previously discovered copper sulfate treatment effects the survivability and gill histology of channel catfish during an infection with F. columnare.
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Therefore to evaluate the functional effects of treatment with copper sulfate on columnaris disease, we performed RNA sequencing on gill samples from control and copper sulfate-treated catfish either immediately (more susceptible) or 24 hours after (more resistant) copper treatment followed by a challenge with F. columnare. We evaluated the differential gene expression patterns over the time-course of infection between groups with a focus on identifying functional differences in immune function.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136222 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136222 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA561619 ncbi.nlm.nih.gov/bioproject/PRJNA561619 ↗
project · from NCBI GEO
- PubMed 42534987 pubmed.ncbi.nlm.nih.gov/42534987 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- Disease 75% · RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE136222 | 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].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%) |
| 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 |