GEO series

Kidney single cell sequencing results from 10-day unilateral ureteral obstruction mice

GSE264184 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2024/04/19 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 2 samples
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: GSDMD-dependent neutrophil extracellular traps promote macrophage-to-myofibroblast transition and renal fibrosis in obstructive nephropathyCell death & disease · 2022

Summary (written by the submitters)

Renal fibrosis is a common consequence of various progressive nephropathies, including obstructive nephropathy, and ultimately leads to kidney failure. Infiltration of inflammatory cells is a prominent feature of renal injury after draining blockages from the kidney, and correlates closely with the development of renal fibrosis. However, the underlying molecular mechanism behind the promotion of renal fibrosis by inflammatory cells remains unclear.

Read the full summary ↓

Herein, we showed that unilateral ureteral obstruction (UUO) induced Gasdermin D (GSDMD) activation in neutrophils, abundant neutrophil extracellular traps (NETs) formation and macrophage-to-myofibroblast transition (MMT) characterized by α-smooth muscle actin (α-SMA) expression in macrophages. Gsdmd deletion significantly reduced infiltration of inflammatory cells in the kidneys and inhibited NETs formation, MMT and thereby renal fibrosis. Chimera studies confirmed that Gsdmd deletion in bone marrow-derived cells, instead of renal parenchymal cells, provided protection against renal fibrosis. Further, specific deletion of Gsdmd in neutrophils instead of macrophages protected the kidney from undergoing fibrosis after UUO. Single-cell RNA sequencing identified robust crosstalk between neutrophils and macrophages. In vitro, GSDMD-dependent NETs triggered p65 translocation to the nucleus, which boosted the production of inflammatory cytokines and α-SMA expression in macrophages by activating TGF-β1/Smad pathway. In addition, we demonstrated that caspase-11, that could cleave GSDMD, was required for NETs formation and renal fibrosis after UUO. Collectively, our findings demonstrate that caspase-11/GSDMD-dependent NETs promote renal fibrosis by facilitating inflammation and MMT, therefore highlighting the role and mechanisms of NETs in renal fibrosis.

Published in

GSDMD-dependent neutrophil extracellular traps promote macrophage-to-myofibroblast transition and renal fibrosis in obstructive nephropathy

Wang Y, Li Y, Chen Z et al. · Cell death & disease 2022 · PMID 35941120 · doi:10.1038/s41419-022-05138-4

This dataset

Open GSE264184 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 GSE264184_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 PRJNA1101203 and SRA study SRP502194. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 35941120) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

Datasets on a similar topic

GSE299417 RNA sequencing of kidneys of sham-operated mice and mice with unilateral ureteral obstruction (UUO) treated with istradefylline or vehicle 24 samples shares obstruction, unilateral, ureteral, kidney
GSE198962 RNA sequencing of normal and unilateral ureteral obstruction (UUO) operated mouse kidneys 10 samples shares obstruction, unilateral, ureteral, kidney
GSE175412 Single-cell RNA sequencing of adult mouse fibrotic kidney induced by unilateral uretral obstruction 3 samples shares obstruction, unilateral, kidney
GSE36496 Murine Kidney Tissue: Unilateral ureteral obstructed mice vs. Sham control 22 samples shares unilateral, ureteral, kidney
GSE241213 Gene expression profile at bulk (24h, 48h & 72h) and single nucleus (24h) level of mouse right kidney post sham operation and unilateral nephrectomy. 40 samples shares unilateral, kidney
GSE272378 PAD4 deletion inhibited obstruction-induced kidney inflammation and fibrosis 10 samples shares obstruction, kidney
GSE263369 Gene expression in kidney cells after unilateral ischemia-reperfusion 2 samples shares unilateral, kidney
GSE278764 DMM inhibited obstruction-induced renal fibrosis by blunting inflammation and activating PPAR signaling 10 samples shares obstruction

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.