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Comparison of Renal Transcriptome Profiles in Patients with Active Lupus Nephritis Reveals Possible New Mechanisms of Disease Progression

GSE239576 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2025/12/31 Platform GPL28038
At a glance

RNA-seq (gene expression) · human · 21 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
Homo sapiens (human)
Samples
21 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.
Summary (written by the submitters)
To identify factors that influence the progression of lupus nephritis (LN), we performed RNA sequencing on renal biopsy samples obtained from patients with active LN. The renal biopsy pathology followed the classification of the International Society of Nephrology and Renal Pathology Society (ISN/RPS) for 21 lupus nephritis patients: 2 in Class II, 3 in Class III, 10 in Class IV, 5 in Class V, and 1 patient with mixed type LN.
Read the full summary ↓
The duration of disease from onset of systemic lupus erythematosus (SLE) to the onset of lupus nephritis was 26 months. Proteinuria was 2.5 (g/gCr or g/24hr), estimated Glomerular Filtration Rate (eGFR) was 72.9 (ml/min/1.73 m2), Index of activity was 5, and Index of chronicity was 3. Among different gene expression variations, the type I interferon (IFN) signature showed high expression in patients with shorter disease duration, preserved eGFR, and lower Index of chronicity. The type I IFN signature contributes to fibrosis in the tubulointerstitial space and worsens chronic lesions. Early control of the type I IFN signature may limit disease progression. Our results reveal a potential molecular mechanism for active LN and the link between functional and structural changes and differential gene expression observed in patients with early-stage LN.
This dataset
Open GSE239576 in finder → Find more human 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 GSE239576_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 PRJNA999726 and SRA study SRP452068. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
A cohort of 21 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run NU-LN1 … NU-LN21 and carry no group information.

Samples in this study
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.