Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas
Single-cell RNA-seq · human · 11 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 11 samples: 5 × human kidney biopsy, disease, sample vs 4 × Folic acid model, mouse kidney, 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
- Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlasNature genetics · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE291551_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1234133 and SRA study SRP569200. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 5 samples read as cases, 1 as controls.
How we read this: 2 replicated groups read from 11 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.
- GSM8837509 Healthy control, mouse kidney
- GSM8837510 Folic acid model, mouse kidney, biol replicate 1 Folic acid model, mouse…
- GSM8837511 Folic acid model, mouse kidney, biol replicate 2 Folic acid model, mouse…
- GSM8837512 Folic acid model, mouse kidney, biol replicate 3 Folic acid model, mouse…
- GSM8837513 Folic acid model, mouse kidney, biol replicate 4 Folic acid model, mouse…
- GSM8837514 G2NA APOL1 risk allele, mouse kidney
- GSM9057439 human kidney biopsy, disease, sample 1 human kidney biopsy, di…
- GSM9057440 human kidney biopsy, disease, sample 2 human kidney biopsy, di…
- GSM9057441 human kidney biopsy, disease, sample 3 human kidney biopsy, di…
- GSM9057442 human kidney biopsy, disease, sample 4 human kidney biopsy, di…
- GSM9057443 human kidney biopsy, disease, sample 5 human kidney biopsy, di…
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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.