Excel · study · 2026
Transcriptome profiling of USP40-silenced mouse podocytes
Listed in NCBI GEO
USP40 is a deubiquitinating enzyme implicated in podocyte cytoskeletal organization and cellular homeostasis.
Description
To investigate the transcriptional consequences of USP40 depletion, conditionally immortalized mouse podocytes were transfected with two independent USP40-targeting siRNAs (siRNA#1 and siRNA#2) or a non-targeting control siRNA. Three independent biological replicates were prepared for each condition.
Total RNA was extracted 48 hours after transfection, followed by poly(A)+ RNA enrichment and strand-specific library preparation. Paired-end RNA sequencing (2 × 36 bp) was performed on an Illumina NextSeq 500 platform, generating two FASTQ files (R1 and R2) per sample. Sequence reads were aligned to the Mus musculus reference genome (GRCm39), and gene-level raw read counts were generated.
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Differential expression analysis was conducted using DESeq2, and genes with adjusted p-value < 0.1 and |log2 fold change| > 0.3 were considered differentially expressed. To ensure biological robustness, downstream analyses focused on genes commonly altered in both independent siRNA-mediated knockdowns. This dataset provides insight into USP40-dependent transcriptional reprogramming toward an injury-prone, cytoskeleton-remodeling state in podocytes.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE322nnn/GSE322762 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE322762 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1431441 ncbi.nlm.nih.gov/bioproject/PRJNA1431441 ↗
project · from NCBI GEO
- PubMed 42068752 pubmed.ncbi.nlm.nih.gov/42068752 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Mus musculus
- 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 | GSE322762 | 13 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: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 |