Evidence map›Paper›PMID 41293966›Full record

ArticleDevelopment (Cambridge, England)2025

Integration of spatial and single-nucleus transcriptomics to map gene expression in the developing mouse kidney.

Christopher P Chaney, Alexandria N Fusco, Elyse D Grilli, Jane N Warshaw, Peter M Luo, Ondine Cleaver, Denise K Marciano, Thomas J Carroll

Abstract read
In one paragraph

Article in Development (Cambridge, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. The kidney stroma in development and disease.Nature reviews. Nephrology · 2025
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Christopher P ChaneyDepartment of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.ORCID 0000-0002-4144-4180
Alexandria N FuscoDepartment of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Elyse D GrilliDepartment of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Jane N WarshawDepartment of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Peter M LuoDepartment of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Ondine CleaverDepartment of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Denise K MarcianoDepartment of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Thomas J CarrollDepartment of Internal Medicine, Division of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.ORCID 0000-0002-8322-4928

Funding

Coordinating and Bioinformatics Unit for the MMPC/DiaCompU24DK076169 · NIDDK · AUGUSTA UNIVERSITY · PI MCINDOE, RICHARD A. · 2006 to 2018
$42.4M
Application of Progenitor Niche Signals to Ex Vivo NephrogenesisRC2DK125960 · NIDDK · ROGOSIN INSTITUTE · PI CARROLL, THOMAS JOSEPH, CLEAVER, ONDINE B · 2021 to 2025
$7.4M
UT Southwestern NORCP30DK127984 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI JAY D. HORTON · 2022 to 2026
$7.4M
Engineering erythropoietin-producing cellsR24DK106743 · NIDDK · ROGOSIN INSTITUTE · PI CARROLL, THOMAS JOSEPH, CLEAVER, ONDINE B · 2015 to 2019
$7.0M
Identifying pathways required for integration of kidney organoid and host epitheliaUC2DK126021 · NIDDK · MOUNT DESERT ISLAND BIOLOGICAL LAB · PI DRUMMOND, IAIN A., MARCIANO, DENISE K · 2020 to 2024
$3.1M
The Role of Renal Interstitium in Kidney DevelopmentR01DK127634 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI CARROLL, THOMAS JOSEPH, PARK, JOO-SEOP · 2021 to 2024
$2.8M
Mechanisms of Disease and Translational ScienceT32GM131945 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI Thomas Joseph Carroll · 2019 to 2026
$1.7M
Interactions between the stroma and progenitor cells during kidney developmentR01DK095057 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI CARROLL, THOMAS JOSEPH · 2013 to 2016
$1.4M
Renal vascular remodeling and arteriogenesis: cues from smooth muscle progenitor cellsR01DK124393 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI CLEAVER, ONDINE B · 2020 to 2023
$1.4M
Application of Progenitor Niche Signals to Ex Vivo NephrogenesisR56DK125960 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI CARROLL, THOMAS JOSEPH, CLEAVER, ONDINE B · 2020 to 2020
$530k
NIDDK/DiaComp DK076169NIDDK NIH HHS DK076169NIDDK NIH HHS P30 DK127984NIDDK NIH HHS R01 DK095057NIDDK NIH HHS R01 DK124393NIDDK NIH HHS R01 DK127634NIDDK NIH HHS R01DK127634NIDDK NIH HHS R24 DK106743NIDDK NIH HHS R56 DK125960NIDDK NIH HHS RC2 DK125960NIDDK NIH HHS RC2DK125960NIDDK NIH HHS U24 DK076169NIDDK NIH HHS UC2 DK126021NIGMS NIH HHS T32 GM131945NIH/NIDDK R01DK127634NIH/NIDDK RC2DK125960University of Texas Southwestern Medical Center
6 · The paper itself

Abstract

The kidney is a complex organ requiring tightly coordinated interactions between epithelial, endothelial and mesenchymal cells during development. Congenital kidney defects can result in kidney disease and renal failure, highlighting the importance of understanding kidney formation mechanisms. Advances in RNA sequencing have revealed remarkable cellular heterogeneity, especially in the kidney stroma, although relationships between stromal, epithelial and endothelial cells remain unclear. This study presents a comprehensive gene expression atlas of embryonic and postnatal kidneys, integrating single-nucleus and in situ RNA sequencing data. We developed the Kidney Spatial Transcriptome Analysis Tool (KSTAT), enabling researchers to identify cell locations, predict cell-cell communication and map gene pathway activity. Using KSTAT, we were able to uncover significant heterogeneity among embryonic kidney pericytes, providing an important resource for hypothesis generation and advancing knowledge of kidney development and disease.

Indexed as

Cell NucleusGene Expression ProfilingGene Expression Regulation, DevelopmentalKidneyTranscriptomeAnimalsMiceOrganogenesisPericytesSequence Analysis, RNASingle-Cell AnalysisCell communicationKidney developmentSingle-nucleus RNA sequencingSpatial transcriptomics

Identifiers

PMID41293966
PMCPMC12772959

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.