Excel · study · 2026
highly throughout RNA sequncing analysis of WT and SDC4-KD endothelium stimulated by TNF-a
Listed in NCBI GEO
To identify downstream molecules and signaling pathways regulated by SDC4 during endothelial inflammatory activation, RNA sequencing (RNA-seq) was performed following SDC4 knockdown in TNF-α-stimulated endothelial cells.
Description
In this project, differentially expressed genes were identified using a threshold of fold change ≥ 2 (i.e., |log₂(fold change)| ≥ 1) and a q-value < 0.05 (where q-value represents the false discovery rate-adjusted p-value).
Based on these criteria, differentially expressed genes, enrichment analyses, gene set enrichment analysis (GSEA), and alternative splicing events were obtained across the designated comparison groups. Principal component analysis (PCA) demonstrated clear separation between the TNF-α group and the TNF-α + SDC4 KD group, indicating substantial transcriptional differences between the two experimental conditions without obvious outlier samples.
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Differential expression analysis identified a total of 1,685 differentially expressed genes (DEGs) between the two groups (FPKM mean ≥ 0.5, |logFC| > 1, P < 0.05), including 775 upregulated genes and 910 downregulated genes following SDC4 knockdown. Hierarchical clustering analysis further demonstrated strong intragroup consistency and distinct intergroup transcriptional profiles, suggesting that SDC4 knockdown notably altered endothelial inflammatory gene expression patterns.
To explore the biological significance of these DEGs, GO and KEGG enrichment analyses were subsequently performed. The enriched pathways were strongly associated with leukocyte transendothelial migration, inflammatory response regulation, and cellular response to inflammatory stimuli.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE346nnn/GSE346259 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE346259 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1524250 ncbi.nlm.nih.gov/bioproject/PRJNA1524250 ↗
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 | GSE346259 | 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 |