GEO series

Loss of Gak leads to lysosome dysfunction and immune modulation in podocytes

GSE302106 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/06/18 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 4 × GAK_C62 biol vs 4 × GAK_KO biol vs 4 × GAK_WT 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.

Summary (written by the submitters)

Lysosome impairment causes cellular and organ dysfunction, highlighting its crucial role in homeostasis. In this study, we uncovered the indispensable role of cyclin G-associated kinase (GAK) in maintaining podocyte lysosome integrity. We previously showed that podocyte-specific loss of Gak (Gak-KO) leads to severe proteinuria, podocyte injury, and kidney failure.

Read the full summary ↓

To identify which GAK domains are necessary for its function, we used a transgenic mouse expressing a truncated 62-kDa C-terminal GAK protein (GAK C62). Our findings showed significant accumulation of autophagic vesicles in Gak-KO podocytes, attributed to impaired lysosomal degradation secondary to lysosomal hydrolase mistrafficking. Notably, GAK C62 expression completely rescued these phenotypes at both cellular and organismal levels. Moreover, in vivo RNA-seq and cytokine profiling demonstrated enrichment of immune-related pathways and IL-11 production in Gak-KO podocytes. Overall, this study underscores the importance of lysosome integrity and suggests how its dysfunction may lead podocytes to adopt immune-like properties, with potential autocrine and paracrine effects within the kidney.

This dataset

Open GSE302106 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 GSE302106_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 PRJNA1288537 and SRA study SRP599260. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

4 × GAK_C62 biol vs 4 × GAK_KO biol vs 4 × GAK_WT biol

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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

GSM9096288 GAK_C62 biol rep 1 GAK_C62 biol
GSM9096289 GAK_C62 biol rep 2 GAK_C62 biol
GSM9096290 GAK_C62 biol rep 3 GAK_C62 biol
GSM9096291 GAK_C62 biol rep 4 GAK_C62 biol
GSM9096292 GAK_KO biol rep 1 GAK_KO biol
GSM9096293 GAK_KO biol rep 2 GAK_KO biol
GSM9096294 GAK_KO biol rep 3 GAK_KO biol
GSM9096295 GAK_KO biol rep 4 GAK_KO biol
GSM9096296 GAK_WT biol rep 1 GAK_WT biol
GSM9096297 GAK_WT biol rep 2 GAK_WT biol
GSM9096298 GAK_WT biol rep 3 GAK_WT biol
GSM9096299 GAK_WT biol rep 4 GAK_WT biol

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.