Mus musculus
Protocols: 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).
ENA first public
2026-03-19
INSDC center name
Department of Gynecology and Obstetrics
INSDC status
public
Submitter Id
E-MTAB-15010:Radiation
broker name
ArrayExpress
collection date
not collected
common name
house mouse
developmental stage
adult
genotype
WAP-T-NP8; WAP-mutp53H270H
geographic location (country and/or sea)
not collected
individual
Tumor
isolate
not applicable
organism part
breast
sample name
E-MTAB-15010:Radiation
scientific_name
Mus musculus
sex
female
strain
BALB/c