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| Status |
Public on Oct 26, 2023 |
| Title |
Spatial Transcriptomic profiling of day2 wounds and intact tissues of Hgfac WT and KO mice |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Wound healing is orchestrated by a spatial and temporal network of intercellular communication between epithelial cells, the stromal compartment, and the immune system. Our scRNA-seq analysis of Hgfac WT and KO wounds reveals that Aldh1a3 is downstream of the HGFAC system and Aldh1a3 is highly upregulated in wound-asociated epithelial (WAE) cells in responce to endoscopic wounding, suggesting WAE cells can potentially secrete retinoic acid into wound bed. To dissect the healing responce in the intestinal mucosa, we peformed spatial transcriptomics analysis.
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| Overall design |
Day2 colonic wounds and intact colon samples from Hgfac WT and KO mice embedded into O.C.T. were used for Visium spatial transcriptomics.
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| Web link |
https://www.science.org/doi/10.1126/scitranslmed.adg5252
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| Contributor(s) |
Nakata T, Segerstolpe Å, Li C, Graham D |
| Citation(s) |
37878672 |
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| Submission date |
Jun 26, 2023 |
| Last update date |
Oct 27, 2023 |
| Contact name |
Ramnik Xavier |
| E-mail(s) |
xaviergeo@broadinstitute.org
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| Organization name |
Broad Institute of MIT and Harvard
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| Lab |
Xavier Lab
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (3) |
| GSM7508783 |
Hgfac WT intact tissues, 3 biological reps |
| GSM7508784 |
Hgfac WT day2 wounds, 3 biological reps |
| GSM7508785 |
Hgfac KO day2 wounds, 3 biological reps |
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| This SubSeries is part of SuperSeries: |
| GSE235743 |
Genetic vulnerability to healing reveals a spatially resolved epithelial restitution program |
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| Relations |
| BioProject |
PRJNA987549 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235742_RAW.tar |
38.9 Mb |
(http)(custom) |
TAR (of CSV, JPG, JSON, MTX, PNG, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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