title: Basal-like breast cancer stimulates MUC1 to support an epithelial/mesenchymal hybrid state and survive radiotherapy
library_construction_protocol: Tumor samples were embedded in cryomatrix, sectioned at 10 µm thickness using a Leica cryostat, and mounted onto Visium Spatial Gene Expression Slides (PN-2000233). Slide Serial Number: V21S08-020-A1 Upon harvest, tumors were fractionated into three pieces to accommodate different types of analyses. One piece was fixed and paraffin-embedded for immunohistochemistry. Another piece was embedded in OCT Embedding Matrix for spatial transcriptomic analyses and immunofluorescence stainings. The third piece was snap-frozen for bulk transcriptomic analyses, optimizing RNA preservation tailored to each specific application. 1x10^6 pH8N8 tumor cells were orthotopically implanted into the right abdominal mammary gland of syngeneic female WAP-T-NP8 mice. The mice were housed under standard laboratory conditions with controlled temperature and humidity, and they were given ad libitum access to food and water. When tumor volumes reached 300 mm³, four female mice (average body mass 25.8±4.6 g, age 131.4±42.1 days) received irradiation with the XCELL RS225 device. The total dose of 11 Gy was administered as 1.1 Gy daily for 5 days, followed by 2 resting days, and another 5 days of 1.1 Gy. Five untreated tumor-bearing mice (average body mass 25.7±6.5 g, age 118.9±44.4 days) served as controls, evaluating the irradiation effects on tumor development. Tumors were harvested 24H after the last treatment. Standard pre-processing steps included log-normalization, scaling, and dimensionality reduction, which were applied to ensure data comparability and enhance the quality of spatial transcriptomic analyses. RNA was extracted from the cryosections using the Visium Spatial Gene Expression kit following the manufacturer's instructions, specifically optimized for spatial transcriptomics applications.  cDNA libraries were constructed using the Visium Spatial Gene Expression Kit, following the manufacturer's protocol (Rev A). 