Omics · study · 2026
RNASeq dataset of human chondrocytes treated with caspase-1 and -8 inhibitors under osteoarthritis-like conditions
Listed in NCBI GEO
About 655 million persons worldwide are affected by osteoarthritis (OA), associated with excruciating chronic pain and disability in the elderly.
Description
Inflammation and cell death are two key events in OA and also key canonical functions of caspases. Since caspases play an important role in modulating inflammation, caspase inhibitors have been widely utilized to study diseases involving inflammation in animal models and clinical trials.
Among these, key caspases, which are responsible for activation of the corresponding pathways include caspase-8 for the receptor mediated apoptotic pathway and caspase-1 as the key inflammatory caspase being involved in OA pathogenesis. OA- and non-OA chondrocytes were treated with caspase-1 and -8 inhibitors and TNFa. RNA was isolated after 3 days and processed for RNA sequencing.
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Data was pre-processed and analysed with R programming language v4.2.2. Downstream analysis included identification of differentially expressed genes providing a comprehensive overview of unique and shared transcriptional changes in both OA and non-OA cohorts. For technical validation RNA integrity was assessed and RNA-seq raw data were processed using Trimmomatic (SE mode) for adapter trimming and quality filtering.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE328nnn/GSE328723 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE328723 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1456412 ncbi.nlm.nih.gov/bioproject/PRJNA1456412 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE328723 | 14 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[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 |