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| Status |
Public on Jun 27, 2024 |
| Title |
Histopathological-based analysis of human kidney spatial transcriptomics data: toward precision pathology |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
In this study, we conducted a histopathological-based analysis of 10x Genomics Visium spatial transcriptomics data on a human kidney sample corresponding as closely as possible to the reality of the interpretation of a kidney biopsy in a healthcare or research context.
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| Overall design |
A kidney specimen from a 33-year-old deidentified patient with chronic kidney disease (CKD) as a consequence of diabetic and hypertensive nephropathy was used for analysis. Utilizing the H&E- and PAS-stained bright-field mosaics as references, a kidney pathologist (PI) conducted morphological-based clustering for each spatially-resolved spot on the Visium slide. This involved manually outlining each kidney morphological structure and/or lesion for the purpose of cluster identification.
A GitHub repository containing the R, Julia, and Python scripts we wrote for the main and supplemental figures can be found at:
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| Web link |
https://github.com/BuilderPie/Human_DKD_Visium
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| Contributor(s) |
Isnard P, Li D, Wu H, Humphreys BD |
| Citation(s) |
39097165 |
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| Submission date |
Mar 13, 2024 |
| Last update date |
Aug 28, 2024 |
| Contact name |
Dian Li |
| E-mail(s) |
dianli@wustl.edu
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| Organization name |
Washington University in St. Louis School of Medicine
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| Department |
Nephrology / Medicine
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| Lab |
Benjamin D. Humphreys Lab
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| Street address |
660 S. Euclid Ave., CB 8118
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA1087410 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE261545_RAW.tar |
81.9 Mb |
(http)(custom) |
TAR (of CSV, H5, JPG, JSON, MTX, PNG, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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