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| Status |
Public on May 04, 2023 |
| Title |
A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Kidney stone disease causes significant morbidity and increases health care utilization. The pathogenesis of stone disease is incompletely understood, due in part to the poor characterization of the cellular and molecular makeup of the human papilla and its alteration with disease. In this work, we characterize the human renal papilla in health and calcium oxalate stone disease using single nuclear RNA sequencing, spatial transcriptomics and high-resolution large scale multiplexed 3D and Co-Detection by indexing (CODEX) imaging. We define and localize subtypes of principal cells enriched in the papilla as well as immune and stromal cell populations. We further uncovered an undifferentiated epithelial cell signature in the papilla, particularly during nephrolithiasis.
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| Overall design |
Frozen 10 µm sections were mounted on to etched frames of the Visium spatial gene expression (VSGE) slides with capture areas according to 10x Genomics protocols (Visium Spatial Protocols—Tissue Preparation Guide, Document Number CD=G000240 Rev A, 10x Genomics). H&E-stained sections were imaged with a Keyence BZ-X810 microscope equipped with a Nikon 10× CFI Plan Fluor objective at 0.7547 um/pixel and camera dimensions of 1920x1440. Stained tissues were permeabilized for 12 minutes. mRNA bound to oligonucleotides on the capture areas of the Visium slides was extracted. cDNA libraries were prepared with second strand synthesis and sequenced utilizing the NovaSeq 6000 Sequencing system (Illumina) in the 28 bp + 120 bp paired-end sequencing mode. Samples were mapped using Space Ranger 1.2.0 with the reference genome GRCh3-2020-A. The data were normalized by SCTransform and merged to build a unified UMAP and dataset.
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| Contributor(s) |
Eadon MT, El-Achkar TM, Ferreira RM, Cheng Y |
| Citation(s) |
37468493 |
| Submission date |
Jun 16, 2022 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Michael T Eadon |
| Organization name |
Indiana University
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| Street address |
950 W Walnut St
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| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE231630 |
A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease |
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| Relations |
| BioProject |
PRJNA849988 |
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