GEO series

CAR-T cell therapy for chronic kidney disease

GSE287413 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/01/19 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 12 samples: 3 × DOCA_salt+mPDGFRβ_CAR-T vs 3 × DOCA_salt+Vec-T vs 3 × DOCA_salt vs 3 × ShamGroups 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: Targeting ECM-producing cells with CAR-T therapy alleviates fibrosis in chronic kidney diseaseCell stem cell · 2025

Summary (written by the submitters)

Kidney fibrosis is a hallmark of chronic kidney disease (CKD) and a potential therapeutic target. However, clinical interventions and therapies targeting kidney fibrosis remain conceptual and practical challenges due to the complex origin, functional heterogeneity and regulation of scar-forming cells.

Read the full summary ↓

Here, we used single cell sequencing technology to identify cell-surface antigens that are broadly and specifically expressed at high levels in kidney cell types that produce extracellular matrix (ECM) during CKD, and study the therapeutic effect of CART therapy targeting the major ECM-producing cell types on kidney fibrosis, which provides a comprehensive treatment strategy for multi-organ fibrosis and its cardiovascular complications in CKD mice.

Published in

Targeting ECM-producing cells with CAR-T therapy alleviates fibrosis in chronic kidney disease

Zhao S, Li R, Xia Y et al. · Cell stem cell 2025 · PMID 40848726 · doi:10.1016/j.stem.2025.07.014

This dataset

Open GSE287413 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 GSE287413_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1212718 and SRA study SRP558339. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40848726) ↗

Study design

3 × DOCA_salt+mPDGFRβ_CAR-T vs 3 × DOCA_salt+Vec-T vs 3 × DOCA_salt vs 3 × Sham

Supports a between-group comparison across 12 samples.

How we read this: 4 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

GSM8745394 DOCA_salt+mPDGFRβ_CAR-T-1 DOCA_salt+mPDGFRβ_CAR-T
GSM8745395 DOCA_salt+mPDGFRβ_CAR-T-2 DOCA_salt+mPDGFRβ_CAR-T
GSM8745396 DOCA_salt+mPDGFRβ_CAR-T-3 DOCA_salt+mPDGFRβ_CAR-T
GSM8745397 DOCA_salt+Vec-T-1 DOCA_salt+Vec-T
GSM8745398 DOCA_salt+Vec-T-2 DOCA_salt+Vec-T
GSM8745399 DOCA_salt+Vec-T-3 DOCA_salt+Vec-T
GSM8745400 DOCA_salt-1 DOCA_salt
GSM8745401 DOCA_salt-2 DOCA_salt
GSM8745402 DOCA_salt-3 DOCA_salt
GSM8745403 Sham-1 Sham
GSM8745404 Sham-2 Sham
GSM8745405 Sham-3 Sham

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