Journal: Matrix Biology Plus
Article Title: Whole organism profiling of the Timp gene family
doi: 10.1016/j.mbplus.2023.100132
Figure Lengend Snippet: Cardiac tissue expression of Timp family members. (A) UMAP clustering of murine cardiac tissue transcriptomes illustrating and (B) the tissue-wide expression patterns of Timps1-3. (C). Violin plots describing several key cell-types with appreciable Timp expression levels in cardiac tissue. (D) Visual interpretation of endothelial cell UMAPs for Timp3 and Timp4 in heart tissue, with the highlighted Timp4 + supercluster and comparison of the differentially expressed (DE) genes, DE matrisome genes, and altered pathways across the identified Timp high and Timp low superclusters. DE gene lists are filtered with adjusted p-values < 0.05, with no fold change threshold applied. (E) RNA in-situ hybridization (RNA ISH) for Timp2 (Cy3 – Green) and Timp4 (Cy5 – Magenta) reveals the spatial distribution of Timp2/4 expression across the cardiac parenchyma. Grey-scaled regions of autofluorescence (FITC channel) are indicated. Cd34 expression was also assessed via IHC in an adjacent tissue section. (F) Due to high autofluorescence in the first animal, a new heart was collected for RNA ISH and IHC for the assessment of Timp4 RNA (Cy5 – Magenta) and Cd34 protein abundance (Alexa Fluor 488 – Green), with an analogous region analyzed by IHC for Cd34 expression. (G) RNA ISH for Timp2 and Timp4 in cardiac vasculature, with a corresponding region analyzed via hematoxylin and eosin staining. In fluorescence images, DAPI staining is represented as blue nuclei. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Article Snippet: The following primary antibodies were used for detection: TIMP1 (Cell Signaling Technology, USA) at 1:500 dilution, TIMP2 (R&D Systems; AF971) 1:500, and TIMP3 (Cell Signaling Technology, USA) 1:750.
Techniques: Expressing, Comparison, RNA In Situ Hybridization, Quantitative Proteomics, Staining, Fluorescence
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