Orthotopic 4T1 tumors spatial transcriptomics

4T1 tumors, 4 weeks after implantation were excised and analyzed using the 10X Visium technology. Overall design: FFPE tissue blocks were cut down to approximately 6.5 mm x 6.5 mm in size and sectioned onto the capture areas of the Visium slide according to 10X Genomics Tissue Preparation Guide CG000408. Slides were then deparaffinized and H&E-stained according to the 10X Genomics Demonstrated Protocol CG000409 and imaged at the Animal & Tissue Imaging Core Facility at CSHL. After imaging, the tissue was decrosslinked and probe hybridization with the Visium Mouse Transcriptome Probe Kit (PN-1000365, 10X Genomics) was performed overnight at 50°C. Probe ligation, probe release and extension, and library preparation were performed according to manufacturer's instructions, and final libraries were sequenced on a NextSeq 500 to target 20,000 reads per spot. Sequencing data were processed with Space Ranger version 2.0.0 (10X Genomics).