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Transcriptome profiling of USP40-silenced mouse podocytes

GSE322762 Mus musculus (mouse) RNA-seq (gene expression) 9 samples Submitted 2026/05/01 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 9 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
9 samples: 3 × Mouse podocyte control siRNA biol vs 3 × Mouse podocyte USP40 siRNA#1 biol vs 3 × Mouse podocyte USP40 siRNA#2 biolGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
USP40 protects podocytes by deubiquitylating integrin β1Biochemical and biophysical research communications · 2026
Summary (written by the submitters)
USP40 is a deubiquitinating enzyme implicated in podocyte cytoskeletal organization and cellular homeostasis. 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.
Read the full summary ↓
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. 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.
Published in
USP40 protects podocytes by deubiquitylating integrin β1
Mikami N, Fukushima T, Takematsu H et al. · Biochemical and biophysical research communications 2026 · PMID 42068752 · doi:10.1016/j.bbrc.2026.153840
This dataset
Open GSE322762 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE322762_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1431441 and SRA study SRP680677. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42068752) ↗
Study design
3 × Mouse podocyte control siRNA biol vs 3 × Mouse podocyte USP40 siRNA#1 biol vs 3 × Mouse podocyte USP40 siRNA#2 biol

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 9 sample titles; they account for 9 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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