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| Status |
Public on Jan 17, 2024 |
| Title |
High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing [10X Visium] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ. We applied direct RNA hybridization-based in situ sequencing (ISS, Cartana) to compare male and female healthy mouse kidneys and the male kidneys injury and repair timecourse of ischemic reperfusion injury (IRI). A pre-selected panel of 200 genes were used to identify the dynamics of cell states and their spatial distributions during injury and repair. We developed a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting atlas allowed us to resolve distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. Projection of snRNA-seq dataset from the same injury and repair samples allowed us to impute the spatial localization of genes not directly measured by Cartana.
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| Overall design |
Kidney spatial transcriptomics data were generated by RNA hybridization-based in situ sequencing (ISS, Cartana) and 10X Visium
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| Contributor(s) |
Humphreys B, Wu H |
| Citation(s) |
38360882 |
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| Submission date |
Mar 09, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Haojia Wu |
| E-mail(s) |
[email protected]
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| Organization name |
Washington University in St. Louis
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| Department |
Renal Division/Internal Medicine
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| Lab |
Humphreys Lab
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| Street address |
600 S Euclid Ave
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| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
MO 63110 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE227046 |
High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing |
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| Relations |
| BioProject |
PRJNA942953 |
