Raw data

SusztakLab raw data files

Everything behind the browsers on this site, in the public repositories where it lives permanently: 32 summary-statistics and association files on figshare, 81 GEO series with raw reads and processed matrices, 10 Zenodo records with single-cell and spatial objects, histology and supplementary tables, the supplementary tables of the 20 source papers, our GWAS Catalog accessions, and the analysis code. All of it is free for non-commercial research under the data use agreement; please cite the paper named with each deposit and the SusztakLab Biobank (susztaklab.com).

figshare · GEO · Zenodo · Paper supplements · GWAS Catalog · Code

figshare 32 files GEO 81 series Zenodo 10 records Paper supplements 20 papers GWAS Catalog 4 Code 4

Summary statistics and association tables (figshare)

GWAS summary statistics, eQTL, pQTL, meQTL, eQTM, allele-specific expression and accessibility tables and the Genetic Scorecard, from 5 laboratory deposits. Every link is a direct download; large files are gzip-compressed text. Genome build is GRCh37 (hg19) unless the file name says otherwise.

Summary statistics of human kidney pQTL and eQTL associations

figshare · 2025 · DOI 10.6084/m9.figshare.30156553.v1 · 2 files, 8.6 MB · cite Hirohama et al., Nature Medicine 2025

kidney_pQTL_summary.txt.gz2.3 MB
kidney_eQTL_summary.txt.gz6.3 MB

Kidney Multiome-based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants (Datasets)

figshare · 2025 · DOI 10.6084/m9.figshare.26299093.v3 · 12 files, 3 GB · cite Liu et al., Science 2025

eGFRcrea GWAS, European ancestry (N = 1,785,582)eGFRcrea_GWAS_EUR_1.7M_Individuals_Summary_Statistics.txt.gz524.6 MB
eGFRcrea GWAS, African ancestry (N = 67,943)eGFRcrea_GWAS_AFR_67K_Individuals_Summary_Statistics.txt.gz673.4 MB
eGFRcrea GWAS, multiancestry (N = 2,287,877) summary statisticseGFRcrea_GWAS_Multi_2.2M_Individuals_Summary_Statistics.txt.gz672.9 MB
Glomerular allele-specific expression, 522 samples, significant associationsASE_RASQUAL_522_Glomeruli_Significant_Associations.txt.gz76.3 MB
Tubular allele-specific expression, 613 samples, significant associationsASE_RASQUAL_613_Tubule_Significant_Associations.txt.gz76.2 MB
Bulk allele-specific accessibility (bASA), 82 kidneysbASA_RASQUAL_82_Kidney_Significant_Associations.txt.gz35.8 MB
Open4Gene peak-to-gene associations, significant (FDR < 0.01)Open4Gene_62K_Cells_Peak_to_Gene_Significant_Associations.txt.gz17.2 MB
Open4Gene peak-to-gene associations, summary statisticsOpen4Gene_62K_Cells_Peak_to_Gene_Summary_Statistics.txt.gz616.5 MB
Cell-type allele-specific accessibility (snASA), 237K cellssnASA_237K_Cells_Significant_Associations.txt.gz1.1 MB
eGFRcrea GWAS, East Asian ancestry (N = 282,852)eGFRcrea_GWAS_EAS_282K_Individuals_Summary_Statistics.txt.gz260.6 MB
snATAC-resolved open chromatin peaks, 96 kidneys, 62,278 cells, 19 cell typesHuman.Kidney.OpenChromatin.snATAC.resolved.ATAC.Peaks.bed.gz4 MB
Genome_wide.Kidney.Disease.Genetic.Scorecard.xlsx63.1 MB

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease (Data Set)

figshare · 2023 · DOI 10.6084/m9.figshare.15183495.v9 · 6 files, 1.1 GB · cite Liu et al., Nature Genetics 2022

Kidney eQTM (N = 414), 175,491 significant CpG–gene pairs (FDR < 0.05)Kidney.eQTM.S414.Significant.CpGlevel.FDR0.05.txt.gz4.2 MB
Kidney meQTL (N = 443), 13,771,378 significant SNP–CpG pairs (q < 0.01)Kidney_meQTL_S443_Significant.q0.01.txt.gz509.6 MB
Kidney eQTL meta-analysis (N = 686), 1,179,179 significant SNP–gene pairs (q < 0.01)Kidney_eQTL_Meta_S686_Significant.q0.01.txt.gz27.3 MB
90,950 significant eGFRcrea variants with eGFRcys and BUN validationeGFRcrea_GWAS_S1.5million_Significant_Variants.txt.gz5.2 MB
eGFRcrea GWAS meta-analysis summary statisticseGFRcrea_GWAS_S1.5million_Summary_Statistics.txt.gz522.4 MB
snATAC_Peaks_Each_CellType.tar.gz13.3 MB

Susztak Lab Datasets

figshare · 2022 · DOI 10.6084/m9.figshare.21604026.v3 · 10 files, 368.4 MB · cite Sheng et al., Nature Genetics 2021

Blood MWAS with hemoglobin A1cBlood_meQTL.FinalA1cSum.txt.gz5 MB
Blood MWAS with albuminuriaBlood_meQTL.FinalAlbuSum.txt.gz12.3 MB
Blood MWAS with eGFRBlood_meQTL.FinaleGFRSum.txt.gz12.9 MB
Blood MWAS with eGFR slopeBlood_meQTL.FinalSlpSum.txt.gz5 MB
Blood mQTL, 12,354,191 significant SNP–CpG pairs (FDR < 0.05)Blood_meQTL.mqtlFinalSum.txt.gz271 MB
Glomerular eQTL (N = 119), significant pairs (FDR < 0.05)Kidney_eQTL.CXGlomsigeQTLsFormated.txt.gz8.6 MB
Tubule eQTL (N = 121), significant pairs (FDR < 0.05)Kidney_eQTL.CXTubsigeQTLsFormated.txt.gz7.2 MB
Kidney_eQTL.FormatedeQTLcis.txt.gz747 KB
Glomerular eQTL (N = 303), significant pairs (FDR < 0.05)Kidney_eQTL.GlomsigeQTLsFormated.txt.gz23.2 MB
Tubule eQTL (N = 356), significant pairs (FDR < 0.05)Kidney_eQTL.TubsigeQTLsFormated.txt.gz22.4 MB

Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments

figshare · 2021 · DOI 10.6084/m9.figshare.14718015.v1 · 2 files, 45.6 MB · cite Sheng et al., Nature Genetics 2021

GlomsigeQTLsFormated.txt.gz23.2 MB
TubsigeQTLsFormated.txt.gz22.5 MB

Sequencing data (Gene Expression Omnibus)

81 series (1,397 samples) with Susztak as a contributing author, from the 2004 diabetic nephropathy arrays to the 2026 CUT&RUN and spatial data: bulk and single-cell RNA-seq, snATAC-seq, ChIP-seq, whole-genome bisulfite and methylation arrays in human, mouse, rat and fly. Retrieved from GEO DataSets (Susztak[Author]), September 2026. Each accession page holds the raw reads (SRA), processed matrices and the linked paper. Human genotype data are not in GEO; they are available through the controlled-access mechanism described in each paper.

Accession	Series	Organism	Assay	PubMed
2026
GSE306009	ACLY-driven metabolic reprogramming promotes histone acetylation and inflammation-associated fibrosis in chronic kidney disease	mouse	chromatin (ATAC / ChIP / CUT&RUN)6 samples	41990244
GSE319933	Bulk RNA-seq profiling of primary mouse tubular epithelial cells following AdvCre-mediated ELF3 deletion under TNFα and IFNγ stimulation	mouse	RNA / single-cell RNA6 samples	—
GSE319877	Transcriptomic profiling of human RPTECs following TNFα and IFNγ stimulation at early and late time points	human	RNA / single-cell RNA20 samples	—
GSE319848	CUT&RUN profiling of ELF3 and NFKB2 binding landscapes in primary mouse tubular epithelial cells under TNFα and IFNγ stimulation	mouse	chromatin (ATAC / ChIP / CUT&RUN)2 samples	—
GSE278614	Single-Cell Spatial Mapping of Human Kidney Development Reveals Cellular Niches and Lineage Dynamics [CosMx]	human	spatial / other3 samples	—
GSE297989	HNF1B integrates signals in a feed-forward loop driving kidney disease progression [RNAseq_UUOd1]	mouse	RNA / single-cell RNA8 samples	41990178
GSE297988	HNF1B integrates signals in a feed-forward loop driving kidney disease progression [RNAseq_P60d2]	mouse	RNA / single-cell RNA8 samples	41990178
GSE297987	HNF1B integrates signals in a feed-forward loop driving kidney disease progression [ChIPseq_Hnf1b]	mouse	chromatin (ATAC / ChIP / CUT&RUN)5 samples	41990178
GSE233078	Single-cell resolution drug effects on renin-angiotensin-aldosterone blockade in ZSF1 rat diabetic kidney disease	rat	RNA / single-cell RNA11 samples	41563360
2025
GSE283166	Cell-specific Inducible Human APOL1 Risk Variant Expression Cause Hypertension and Renal Damage	mouse	RNA / single-cell RNA6 samples	41376591
GSE291551	Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas	human; mouse	RNA / single-cell RNA11 samples	40775269
2024
GSE273027	Germline TET2 variants contribute to the pathogenesis of kidney disease through impaired DNA damage repair and the activation of cytosolic nucleotide sensors	human; mouse	RNA / single-cell RNA6 samples	—
GSE223777	Transcriptomic analysis of Pepck-Vpr mouse kidney	mouse	RNA / single-cell RNA4 samples	39032602
GSE243871	Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney	human; mouse	RNA / single-cell RNA, chromatin (ATAC / ChIP / CUT&RUN)28 samples	39009564
GSE243870	Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (scRNA-Seq)	mouse	RNA / single-cell RNA3 samples	39009564
GSE243868	Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (snATAC-Seq)	mouse	chromatin (ATAC / ChIP / CUT&RUN)2 samples	39009564
GSE243867	Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (RNA-Seq)	human	RNA / single-cell RNA18 samples	39009564
GSE243866	Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (ChIP-Seq)	human	chromatin (ATAC / ChIP / CUT&RUN)5 samples	39009564
GSE211785	Spatially resolved human kidney multi-omics single cell atlas highlights the key role of fibrotic microenvironment in kidney disease progression.	human	RNA / single-cell RNA, chromatin (ATAC / ChIP / CUT&RUN)80 samples	38217002 38514613 39048792 41376591 40796935
2023
GSE183842	Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism	rat	RNA / single-cell RNA, chromatin (ATAC / ChIP / CUT&RUN)47 samples	37906287
GSE183841	Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [bulk RNA-seq]	rat	RNA / single-cell RNA16 samples	37906287
GSE183840	Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [snATAC-seq]	rat	chromatin (ATAC / ChIP / CUT&RUN)9 samples	37906287
GSE183839	Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [snRNA-seq]	rat	RNA / single-cell RNA22 samples	37906287
GSE242095	Endogenous renal adiponectin drives gluconeogenesis through enhancing pyruvate and fatty acid utilization	mouse	RNA / single-cell RNA6 samples	37848446
GSE220493	Unified Mouse and Human Kidney Single-Cell Expression Atlas Reveal Commonalities and Differences in Disease States	mouse	RNA / single-cell RNA6 samples	—
GSE209821	Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution	rat	RNA / single-cell RNA12 samples	37023747
GSE207587	The RNA-seq for the kidneys injected with cisplatin and NAD precursors.	mouse	RNA / single-cell RNA16 samples	36914909
2022
GSE212715	Tet2 and Tet3 mediated active cytosine hydroxymethylation in Six2 progenitor cells is critical for nephron progenitor differentiation and nephron endowment	mouse	RNA / single-cell RNA, DNA methylation4 samples	—
GSE137570	Loss of FERM domain-containing protein 3 (FRMD3) is associated with severity of chronic kidney disease	human	RNA / single-cell RNA41 samples	36550108
GSE205217	Hepatocyte nuclear factor 1β gene regulation in E14.5 ureteric bud cells	mouse	RNA / single-cell RNA10 samples	36266461
GSE205189	Hepatocyte nuclear factor 1β binding in E14.5 kidney	mouse	chromatin (ATAC / ChIP / CUT&RUN)6 samples	36266461
GSE200547	Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease	human	chromatin (ATAC / ChIP / CUT&RUN)4 samples	35710981 38287030
GSE182256	Single cell analysis identifies the key role of basophils orchestrating Th17 immunity and kidney fibrosis	mouse	RNA / single-cell RNA8 samples	35552540
2021
GSE176465	Urine single cell RNA-sequencing in focal segmental glomerulosclerosis reveals inflammatory signatures in immune cells and podocytes	human	RNA / single-cell RNA23 samples	35155868 36644347
GSE181671	African American-specific APOL1 risk variants in endothelial cells exacerbate sepsis and COVID19 severity	mouse	RNA / single-cell RNA2 samples	41376591
GSE180420	Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration	mouse	RNA / single-cell RNA20 samples	35821371
GSE173343	Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments [RNA-seq]	human	RNA / single-cell RNA68 samples	34385711 38287030 39048792
GSE168676	Identification of dachshund-1 (DACH1) transcriptional target genes in podocytes at baseline and in experimental diabetes	mouse	RNA / single-cell RNA12 samples	33998601
GSE172008	Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments	human	chromatin (ATAC / ChIP / CUT&RUN)2 samples	34385711 34426578 38287030 38287344
GSE166355	Defining the lineage of thermogenic perivascular adipose tissue [Thoracic PVAT]	human; mouse	RNA / single-cell RNA6 samples	33846639
GSE164528	Defining the lineage of thermogenic perivascular adipose tissue	human; mouse	RNA / single-cell RNA42 samples	33846639
GSE164527	Defining the lineage of thermogenic perivascular adipose tissue [PVAT v IWAT]	mouse	RNA / single-cell RNA12 samples	33846639
GSE164526	Defining the lineage of thermogenic perivascular adipose tissue [Pup Aorta]	mouse	RNA / single-cell RNA12 samples	33846639
GSE164525	Defining the lineage of thermogenic perivascular adipose tissue [Adult Aorta]	mouse	RNA / single-cell RNA12 samples	33846639
GSE157640	Urinary single cell profiling captures cellular diversity of the kidney	human	RNA / single-cell RNA18 samples	33531352
2020
GSE156686	Renal proximal tubule cell state and metabolism are coupled by nuclear receptors	mouse	RNA / single-cell RNA8 samples	33301705
GSE152765	Metabolic programming drives proximal tubule differentiation and kidney dysfunction	human	RNA / single-cell RNA1 samples	33301705
GSE157079	Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets	mouse	RNA / single-cell RNA, chromatin (ATAC / ChIP / CUT&RUN)13 samples	33859189 34426578
GSE149638	ASEP: gene-based detection of allele-specific expression cross individuals in a population by RNA sequencing	human	RNA / single-cell RNA96 samples	32392242
GSE145477	Single cell transcriptomics analysis of bone marrow mesenchymal lineage cells	mouse	RNA / single-cell RNA4 samples	32286228 35393948
GSE146974	Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis	human	RNA / single-cell RNA3 samples	32393754 34035047
GSE134267	Dnmt3a and Dnmt3b-mediated decommissioning of fetal enhancers linked to kidney disease	mouse	RNA / single-cell RNA, DNA methylation19 samples	32127410
2019
GSE126823	Ascorbic acid–induced TET activation mitigates adverse hydroxymethylcystosine loss in renal cell carcinoma	human	DNA methylation12 samples	30702441
GSE124610	Loss of hydroxymethylcytosine is an independent adverse prognostic factor in clear cell Renal Cell Carcinoma (ccRCC) and can be abrogated by ascorbic acid mediated TET activation	human	DNA methylation8 samples	30702441
GSE110481	DNMT1 in Six2 progenitor cells is essential for transposable element silencing and kidney development	mouse	RNA / single-cell RNA, DNA methylation15 samples	30850438
2018
GSE115098	Kidney compartment specific eQTL studies highlight causal genes and pathways for renal disease development	human	RNA / single-cell RNA20 samples	30275566 31167971 31451708 34426578 38287030 39048792
GSE104907	ERRγ coordinates a transcriptional program of mitochondrial and renal reabsorptive functions implicated in kidney disease	mouse	RNA / single-cell RNA, chromatin (ATAC / ChIP / CUT&RUN)9 samples	29735694
GSE104906	ERRγ coordinates a transcriptional program of mitochondrial and renal reabsorptive functions implicated in kidney disease [RNA-seq]	mouse	RNA / single-cell RNA15 samples	29735694
GSE104905	ERRγ coordinates a transcriptional program of mitochondrial and renal reabsorptive functions implicated in kidney disease [ChIP-seq]	mouse	chromatin (ATAC / ChIP / CUT&RUN)9 samples	29735694
GSE107585	Comprehensive single cell RNAseq analysis of the kidney reveals novel cell types and unexpected cell plasticity	mouse	RNA / single-cell RNA7 samples	29622724
2017
GSE108106	RNA sequence on the fed and fasted state of kidneys in mice	mouse	RNA / single-cell RNA9 samples	28404638
GSE77432	Alterations in the hepatic epigenome in mice exposed to a maternal high fat diet in utero	mouse	RNA / single-cell RNA, DNA methylation8 samples	28911167
GSE77431	Alterations in the hepatic gene expression in mice exposed to a maternal high fat diet in utero [Microarray]	mouse	RNA / single-cell RNA2 samples	28911167
GSE77430	Alterations in the hepatic epigenome in mice exposed to a maternal high fat diet in utero [HELP]	mouse	DNA methylation6 samples	28911167
GSE81492	APOL1 variant expression in mouse podocytes cause kidney disease	mouse	RNA / single-cell RNA10 samples	28218918 41376591
2016
GSE80384	Notch pathway is overexpressed and is a therapeutic target in clear cell renal cancer	mouse	RNA / single-cell RNA6 samples	27909050
2015
GSE70544	Transcriptional Signatures of Hypoxic and Inflammatory Renal Epithelial Injury	human	RNA / single-cell RNA12 samples	26400545
GSE69815	Expression array of glucosamine-fed Drosophila heart/nephrocyte complexes	fly	RNA / single-cell RNA6 samples	26190114
2014
GSE60119	Next Generation Sequencing Facilitates Quantitative Analysis of Normal Human Kidney Transcriptomes	human	RNA / single-cell RNA2 samples	25231882
GSE49420	Integrative analysis demonstrates widespread NOTCH pathway activation in patients with renal cancer and reveals aberrant DNA methylation that targets the regulatory regions of the kidney genome	human	DNA methylation26 samples	24916699
2013
GSE50874	Methylation Profiling of Human Kidney Tubules	human	DNA methylation85 samples	24098934 28556588
GSE49637	Histone tail modification profiles of human renal tubule epithelial cells	human	chromatin (ATAC / ChIP / CUT&RUN)7 samples	24098934 25007794 28575649
GSE49557	Methylation profiles of Human kidney tubules	human	DNA methylation26 samples	24098934
GSE48944	Gene expression profiles of human kidneys	human	RNA / single-cell RNA25 samples	24098934
2011
GSE30566	Transcriptome Analysis of Human Diabetic Kidney Disease (Control Glomeruli vs. Control Tubuli)	human	RNA / single-cell RNA25 samples	21752957
GSE30529	Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Tubuli vs. Control Tubuli)	human	RNA / single-cell RNA22 samples	21752957
GSE30528	Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Glomeruli vs. Control Glomeruli)	human	RNA / single-cell RNA22 samples	21752957
GSE30122	Transcriptome Analysis of Human Diabetic Kidney Disease	human	RNA / single-cell RNA69 samples	21752957 26190114
2010
GSE12682	Expression data from Human Kidney (HK) samples	human	RNA / single-cell RNA52 samples	19277126
2009
GSE12683	Expression data from Balb/c mice kidney samples	mouse	RNA / single-cell RNA20 samples	19277126
2004
GSE710	diabetic nephropathy streptozotocin db db	mouse	RNA / single-cell RNA50 samples	14988265

Single-cell objects, histology and supplementary data (Zenodo)

Analysis-ready h5ad objects, whole-slide H&E images, supplementary tables and archived code that accompany our papers, each with a DOI (10 records).

Data repository: Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup

Zenodo · Dataset · 2026 · DOI 10.5281/zenodo.19868428 · 2 files, 8.1 GB

Diagnosis.xlsx12.2 KB
spatial_adata_xenium_cosmx_zenodo.h5ad8.1 GB

High-resolution H&E images from the HistoSweep study across multiple tissues and diseases

Zenodo · Dataset · 2026 · DOI 10.5281/zenodo.18165537 · 6 files, 11.7 GB

Spatial Dataset

Zenodo · Dataset · 2025 · DOI 10.5281/zenodo.17965639

Files are listed on the Zenodo record page (embargoed or restricted at the time of listing).

Human Kidney T2D and Normal HE

Zenodo · Image · 2025 · DOI 10.5281/zenodo.17228449 · 1 files, 460.6 MB

kidney_he.jpg460.6 MB

A cross-species single-cell kidney atlas: Data repository

Zenodo · Dataset · 2025 · DOI 10.5281/zenodo.15007208 · 12 files, 29.8 GB

Open4Gene: a hurdle model-based method for peak-to-gene linkage analysis

Zenodo · Software · 2024 · DOI 10.5281/zenodo.12768472 · 1 files, 5.9 MB

hbliu/Open4Gene-v1.0.0.zip5.9 MB

Suppl. Data for ZSF1_RAASi

Zenodo · Dataset · 2023 · DOI 10.5281/zenodo.8189327

Files are listed on the Zenodo record page (embargoed or restricted at the time of listing).

Suppl. Data for ZSF1rat sGC

Zenodo · Dataset · 2022 · DOI 10.5281/zenodo.6950236 · 21 files, 21.5 MB

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease (Code)

Zenodo · Software · 2022 · DOI 10.5281/zenodo.6392494 · 1 files, 17.4 MB

hbliu/Kidney_Epi_Pri-Kidney_Epi_Pri.zip17.4 MB

Paired human macrophage RNA sequencing data

Zenodo · Dataset · 2020 · DOI 10.5061/dryad.866t1g1nb · 1 files, 32.5 MB

macrophage_allele_specific_expression.txt32.5 MB

Supplementary tables and data of the source papers

The 20 papers behind the 30 resources on this site, each with its supplementary tables, supplementary data and source data files (direct downloads from the publisher where available), the free full text at PubMed Central, and the GEO accessions linked to the paper. The supplementary tables often hold the complete result lists (all significant loci, QTLs, differentially expressed genes and cell-type markers) that the browsers summarise.

Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup.

Bernhard Dumoulin, Jonathan Levinsohn, Konstantin A. Klötzer et al. and Katalin Susztak · Dumoulin et al., Nature 2026 · PMID 42056516

Resources on this site: Human Single-Cell Spatial Atlas

Supplementary Figures pdf Supplementary Information pdf Supplementary Tables xlsx Supplementary Data zip Source Data Fig. 2 xlsx Source Data Fig. 3 xlsx Source Data Fig. 4 xlsx Source Data Fig. 5 xlsx Source Data Extended Data Fig. 7 xlsx Source Data Extended Data Fig. 10 xlsx Free full text and supplements (PubMed Central PMC13216073) ↗

Single-cell spatial mapping of human kidney development implicates the microenvironment in guiding cell fate decisions.

Jonathan Levinsohn, Samuel Grindel, Bernhard Dumoulin et al. and Katalin Susztak · Levinsohn, Grindel et al., Nature Genetics 2026 · PMID 42533102

Resources on this site: Human Fetal Kidney Spatial Atlas

Supplementary Information pdf Supplementary Data 1 html Supplementary Tables xlsx Free full text and supplements (PubMed Central PMC13447095) ↗

Single-Cell Resolution Drug Effects of Renin-Angiotensin-Aldosterone Blockade in ZSF1 Rat Diabetic Kidney Disease.

Michael S. Balzer, Jianfu Zhou, Amin Abedini et al. and Katalin Susztak · Balzer et al., J Am Soc Nephrol 2026 · PMID 41563360

Resources on this site: RAAS Inhibition in DKD Atlas

Free full text and supplements (PubMed Central PMC13337198) ↗GSE233078

The proteogenomic landscape of the human kidney and implications for cardio-kidney-metabolic health.

Daigoro Hirohama, João Fadista, Eunji Ha et al. and Katalin Susztak · Hirohama et al., Nature Medicine 2025 · PMID 40796935

Resources on this site: Human Kidney Protein QTL Atlas

Supplementary Information pdf Supplementary Tables xlsx Supplementary Data 1 xlsx Source Data Fig. 1 xlsx Source Data Fig. 2 xlsx Source Data Fig. 3 xlsx Source Data Fig. 4 xlsx Source Data Extended Data Fig. 2 xlsx Source Data Extended Data Fig. 4 xlsx Source Data Extended Data Fig. 7 xlsx Source Data Extended Data Fig. 10 xlsx Free full text and supplements (PubMed Central PMC12435990) ↗GSE211785

Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas.

Konstantin A. Klötzer, Amin Abedini, Shen Li, Michael S. Balzer et al. and Katalin Susztak · Klötzer et al., Nature Genetics 2025 · PMID 40775269

Resources on this site: SISKA · Rodent–Human Gene Expression Coordination

Supplementary Information pdf Supplementary Tables xlsx Source Data Fig. 4 xlsx Source Data Fig. 5 xlsx Source Data Fig. 6 xlsx Source Data Extended Data Fig. 4 xlsx Source Data Extended Data Fig. 8 xlsx Source Data Extended Data Fig.10 xlsx Free full text and supplements (PubMed Central PMC12415535) ↗GSE291551

Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants.

Hongbo Liu, Amin Abedini, Eunji Ha, Ziyuan Ma et al. and Katalin Susztak · Liu et al., Science 2025 · PMID 39913582

Resources on this site: eGFR GWAS (2.2 million) and ScoreCard

Supplementary materials at the journal ↗Free full text and supplements (PubMed Central PMC12013656) ↗

Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression.

Amin Abedini, Jonathan Levinsohn, Konstantin A. Klötzer et al. and Katalin Susztak · Abedini, Levinsohn et al., Nature Genetics 2024 · PMID 39048792

Resources on this site: Human Kidney Disease snATAC-seq · Human Kidney Spatial Transcriptome · Single-Cell Transcriptome (Susztak) · Single-Cell Transcriptome (Susztak and KPMP)

Supplementary Information pdf Supplementary Tables 1–26 xlsx Free full text and supplements (PubMed Central PMC11592391) ↗GSE211785 GSE173343 GSE115098

Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

Amin Abedini, Andrea Sánchez-Navaro, Junnan Wu, Konstantin A. Klötzer et al. and Katalin Susztak · Abedini et al., J Clin Invest 2024 · PMID 37906287

Resources on this site: Rat DOCA gene map · Rat DOCA snATAC-seq (IGV)

Supplementary materials at the journal ↗Free full text and supplements (PubMed Central PMC10760974) ↗GSE183842 GSE183841 GSE183840 GSE183839

Unified Mouse and Human Kidney Single-Cell Expression Atlas Reveal Commonalities and Differences in Disease States.

Jianfu Zhou, Amin Abedini, Michael S. Balzer et al. and Katalin Susztak · Zhou et al., J Am Soc Nephrol 2023 · PMID 37639336

Resources on this site: Mouse Kidney scRNA-seq Atlas

Free full text and supplements (PubMed Central PMC10631616) ↗

Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution.

Michael S. Balzer, Mira Pavkovic, Julia Frederick, Amin Abedini et al. and Katalin Susztak · Balzer et al., Cell Reports Medicine 2023 · PMID 37023747

Resources on this site: Rat DKD snRNA-seq (UMAP)

Free full text and supplements (PubMed Central PMC10140477) ↗GSE209821

Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration.

Michael S. Balzer, Tomohito Doke, Ya-Wen Yang, Daniel L. Aldridge, Hailong Hu, Hung Mai, Dhanunjay Mukhi, Ziyuan Ma, Rojesh Shrestha, Matthew B. Palmer, Christopher A. Hunter and Katalin Susztak · Balzer et al., Nature Communications 2022 · PMID 35821371

Resources on this site: Mouse Kidney IRI scRNA-seq

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease.

Hongbo Liu, Tomohito Doke, Dong Guo, Xin Sheng, Ziyuan Ma, Joseph Park, Ha My T. Vy, Girish N. Nadkarni, Amin Abedini, Zhen Miao, Matthew Palmer, Benjamin F. Voight, Hongzhe Li, Christopher D. Brown, Marylyn D. Ritchie, Yan Shu and Katalin Susztak · Liu et al., Nature Genetics 2022 · PMID 35710981

Resources on this site: eGFRcrea GWAS · Kidney eQTL · Kidney meQTL · Kidney snATAC-seq

Supplementary Information pdf Supplementary Tables xlsx Source Data Fig. 8 pdf Free full text and supplements (PubMed Central PMC11626562) ↗GSE200547

Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis.

Tomohito Doke, Amin Abedini, Daniel L. Aldridge, Ya-Wen Yang, Jihwan Park, Christina M. Hernandez, Michael S. Balzer, Rojesh Shrestha, Gaia Coppock, Juan M. Inclan Rico, Seung Yub Han, Xin Sheng, Adrian M. Piliponsky, Marco Angelozzi, Veronique Lefebvre, Mark C. Siracusa, Christopher A. Hunter and Katalin Susztak · Doke et al., Nature Immunology 2022 · PMID 35552540

Resources on this site: Mouse UUO scRNA-seq

Supplementary Figs. 1–10 pdf Supplementary Tables 1–8 xlsx Free full text and supplements (PubMed Central PMC11783796) ↗GSE182256

Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets.

Zhen Miao, Michael S. Balzer, Ziyuan Ma, Hongbo Liu, Junnan Wu, Rojesh Shrestha, Tamas Aranyi, Amy Kwan, Ayano Kondo, Marco Pontoglio, Junhyong Kim, Mingyao Li, Klaus H. Kaestner and Katalin Susztak · Miao, Balzer et al., Nature Communications 2021 · PMID 33859189

Resources on this site: Developing Kidney scRNA-seq · Developing Kidney snATAC-seq (IGV)

Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments.

Xin Sheng, Yuting Guan, Ziyuan Ma, Junnan Wu, Hongbo Liu, Chengxiang Qiu, Steven Vitale, Zhen Miao, Matthew J. Seasock, Matthew Palmer, Myung K. Shin, Kevin L. Duffin, Steven S. Pullen, Todd L. Edwards, Jacklyn N. Hellwege, Adriana M. Hung, Mingyao Li, Benjamin F. Voight, Thomas M. Coffman, Christopher D. Brown and Katalin Susztak · Sheng et al., Nature Genetics 2021 · PMID 34385711

Resources on this site: Kidney eQTL atlases · Kidney snATAC-seq (IGV)

Supplementary Information pdf Supplementary Tables xlsx Source Data Fig. 2 tif Source Data Fig. 2 xlsx Free full text and supplements (PubMed Central PMC9338440) ↗GSE173343 GSE172008

The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation.

Poonam Dhillon, Jihwan Park, Carmen Hurtado Del Pozo, Lingzhi Li, Tomohito Doke, Shizheng Huang, Juanjuan Zhao, Hyun Mi Kang, Rojesh Shrestha, Michael S. Balzer, Shatakshee Chatterjee, Patricia Prado, Seung Yub Han, Hongbo Liu, Xin Sheng, Pieterjan Dierickx, Kirill Batmanov, Juan P. Romero, Felipe Prósper, Mingyao Li, Liming Pei, Junhyong Kim, Nuria Montserrat and Katalin Susztak · Dhillon, Park et al., Cell Metabolism 2021 · PMID 33301705

Resources on this site: Mouse Folic Acid Nephropathy scRNA-seq

Free full text and supplements (PubMed Central PMC9259369) ↗GSE156686 GSE152765

Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease.

Xin Sheng, Chengxiang Qiu, Hongbo Liu, Caroline Gluck, Jesse Y. Hsu, Jiang He, Chi-Yuan Hsu, Daohang Sha, Matthew R. Weir, Tamara Isakova, Dominic Raj, Hernan Rincon-Choles, Harold I. Feldman, Raymond Townsend, Hongzhe Li and Katalin Susztak · Sheng et al., PNAS 2020 · PMID 33144501

Resources on this site: Human Blood mQTL Atlas

Supplementary materials at the journal ↗Free full text and supplements (PubMed Central PMC7682409) ↗

Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease.

Chengxiang Qiu, Shizheng Huang, Jihwan Park, YoSon Park, Yi-An Ko, Matthew J. Seasock, Joshua S. Bryer, Xiang-Xi Xu, Wen-Chao Song, Matthew Palmer, Jon Hill, Paolo Guarnieri, Julie Hawkins, Carine M. Boustany-Kari, Steven S. Pullen, Christopher D. Brown and Katalin Susztak · Qiu et al., Nature Medicine 2018 · PMID 30275566

Resources on this site: Kidney eQTL (bulk)

Supplementary Text and Figures Supplementary Figures 1–9 and Supplementary Tables 1–4 pdf Free full text and supplements (PubMed Central PMC6301011) ↗GSE115098

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease.

Jihwan Park, Rojesh Shrestha, Chengxiang Qiu, Ayano Kondo, Shizheng Huang, Max Werth, Mingyao Li, Jonathan Barasch and Katalin Susztak · Park et al., Science 2018 · PMID 29622724

Resources on this site: Mouse Kidney scRNA-seq Atlas (UMAP)

Supplementary materials at the journal ↗Free full text and supplements (PubMed Central PMC6188645) ↗GSE107585

Human kidney tubule-specific gene expression based dissection of chronic kidney disease traits.

Pazit Beckerman, Chengxiang Qiu, Jihwan Park, Nora Ledo, Yi-An Ko, Ae-Seo Deok Park, Sang-Youb Han, Peter Choi, Matthew Palmer and Katalin Susztak · Beckerman et al., EBioMedicine 2017 · PMID 28970079

Resources on this site: Bulk Expression and Disease Correlation

Free full text and supplements (PubMed Central PMC5652292) ↗

GWAS Catalog accessions

Study accessions in the NHGRI-EBI GWAS Catalog for genome-wide association studies from the laboratory and its consortia; the catalog provides harmonised summary statistics where available.

GCST90100220 — eGFRcrea GWAS, 1.5 million individuals (European and East Asian ancestry) — full summary statistics · cite Liu et al., Nature Genetics 2022
GCST008747 — eGFR GWAS, Million Veteran Program (Hellwege et al., Nature Communications 2019), combined
GCST008745 — eGFR GWAS, Million Veteran Program, non-diabetic individuals
GCST008746 — eGFR GWAS, Million Veteran Program, individuals with diabetes

Analysis code

Methods developed for these datasets, on GitHub with archived releases on Zenodo.

Open4Gene ↗

Hurdle-model method for peak-to-gene linkage in single-nucleus multiome data (Liu et al., Science 2025). Archived at Zenodo 10.5281/zenodo.12768472.

RsnATACmultiome

github.com

Kidney_Epi_Pri ↗

Kidney epigenome- and transcriptome-based multi-stage prioritization pipeline (Liu et al., Nature Genetics 2022). Archived at Zenodo 10.5281/zenodo.6392494.

prioritizationGWASeQTL

github.com

QDMR ↗

Quantitative differentially methylated region calling for bisulfite sequencing data.

DNA methylation

github.com

SMART2 ↗

Specific Methylation Analysis and Report Tool for bisulfite sequencing platforms.

DNA methylation

github.com

Repository inventories retrieved September 2026 from the GEO, figshare, Zenodo and GWAS Catalog APIs. Missing something you need? Write to ksusztak@pennmedicine.upenn.edu.