Single-nuclei RNA/ATAC-seq of healthy and injured human kidney nephrectomy tissue
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 6 × snRNA-Seq of human kidney, library vs 6 × scATAC-Seq of human kidney, libraryGroups 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
- Multiomic analysis of human kidney disease identifies a tractable inflammatory and pro-fibrotic tubular cell phenotypeNature communications · 2025
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 GSE254185_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1044309 and SRA study SRP473850. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 2 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.
- GSM8035645 snRNA-Seq of human kidney, library1 snRNA-Seq of human kidn…
- GSM8035646 snRNA-Seq of human kidney, library2 snRNA-Seq of human kidn…
- GSM8035647 snRNA-Seq of human kidney, library3 snRNA-Seq of human kidn…
- GSM8035648 snRNA-Seq of human kidney, library4 snRNA-Seq of human kidn…
- GSM8035649 snRNA-Seq of human kidney, library5 snRNA-Seq of human kidn…
- GSM8035650 snRNA-Seq of human kidney, library6 snRNA-Seq of human kidn…
- GSM8035651 scATAC-Seq of human kidney, library1 scATAC-Seq of human kid…
- GSM8035652 scATAC-Seq of human kidney, library2 scATAC-Seq of human kid…
- GSM8035653 scATAC-Seq of human kidney, library3 scATAC-Seq of human kid…
- GSM8035654 scATAC-Seq of human kidney, library4 scATAC-Seq of human kid…
- GSM8035655 scATAC-Seq of human kidney, library5 scATAC-Seq of human kid…
- GSM8035656 scATAC-Seq of human kidney, library6 scATAC-Seq of human kid…
- GSE281526 Single-nuclei RNA-seq and ATAC-seq for Human Retina from Diverse Ancestry Backgrounds 185 samples shares single-nuclei, atac-seq
- GSE233321 Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures 118 samples shares healthy
- GSE275610 scRNA-seq and snATAC-seq reveal differentiation trajectories of several pancreatic islet induction protocols 341 samples shares atac-seq
- GSE300717 RNA-seq and ATAC-seq analysis of 5-azacytidine-treated HepG2 cells reveals epigenetic reactivation of BFL-1 and SQOR in hepatocellular carcinoma 17 samples shares atac-seq
- GSE278751 A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation (Multiome scRNA-seq/scATAC-seq) 14 samples shares atac-seq
- GSE320155 scRNA‑seq of human intra‑hepatic CD4⁺ T cells reveals unique Treg transcriptional identities and two steady‑state tissue‑adaptation programs across healthy and HCC liver samples 60 samples shares healthy
- GSE279480 Longitudinally stable T cell and innate immune activity distinguish healthy adult immunotypes I 1021 samples shares healthy
- GSE314416 Immune-microbiome coordination defines interferon setpoints in healthy humans [CITE-seq and WMS] 108 samples shares healthy
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.