GSM9042317: Mouse, Visium ST, Primary tumor, #9b; Mus musculus; OTHER
The mammary tumors were harvested at different experimental endpoints and processed either for tissue collection and fixation or for scRNA-seq. For ST and IMC, the tissue was fixed in 4% paraformaldehyde immediately after harvesting. The fixed samples were trimmed, embedded in paraffin and stained with H&E for a first histological assessment. For scRNA-seq, the 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v3.1 was used according to the manufacturer's standard protocol (cDNA amplification in 14 cycles). A targeted cell recovery of 8'000 cells per sample was aimed. The sequencing of the library was performed on the NovaSeq 6000 platform (Illumina) using a S4 flow cell. For ST, 5 μm thick tissue sections were placed on Visium slides with the ROI within the capture area and manually H&E stained and scanned with an S360 Nanozoomer (Hamamatsu) using a 40x magnification. cDNA libraries were constructed according to the Visium Gene Expression User Guide (10X Genomics) and sequenced by the Next Generation Sequencing Platform at the University of Bern on an Illumina NovaSeq 6000 System on different flow cells with 100-300 cycles.