Excel · study · 2026
RNA-seq analysis of bEnd.3 cells with shRNA-mediated knockdown of Npc1 versus control
Listed in NCBI GEO
This study aims to elucidate the transcriptional regulatory role of the Npc1 gene in bEnd.3 cells through transcriptome sequencing.
Description
We achieved stable knockdown of Npc1 in bEnd.3 cells using transposon-delivered shRNA, while the control group received non-targeting shRNA (n=3 biological replicates per group). Knockdown efficiency was validated by qRT-PCR (reduction >90%).
Total RNA was extracted and sequenced on the DNBSEQ platform. Differential expression analysis revealed that differentially expressed genes were significantly enriched in pathways related to lipid metabolism and tight junction function, indicating that Npc1 plays a critical role in regulating these cellular processes in bEnd.3 cells. This dataset provides a resource for studying Npc1-dependent gene networks.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE316nnn/GSE316088 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE316088 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1399329 ncbi.nlm.nih.gov/bioproject/PRJNA1399329 ↗
project · from NCBI GEO
- PubMed 42208871 pubmed.ncbi.nlm.nih.gov/42208871 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Mus musculus
- From keywords
- Life Sciences
- Inferred from text
- Genetics 70% · RNA sequencing 65% · Sequencing 75%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE316088 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].anzsrc:group:3105 | 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: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 (65%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:10090 | 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 |