GSM6543817: mouse breast tumor late stage replicate 2; Mus musculus; OTHER
Mouse tissue was processed according to the Visual Spatial Protocol-Tissue Preparation Guide by 10X Genomics. In brief, we flash froze tissue samples in OCT using a Thermo Scientific Thermo-Flask benchtop container filled three quarters with liquid nitrogen and a small, round, metal bowl with 1-inch height worth of isopentane. A pair of sturdy needle-drivers was used to maneuver the isopentane bowl in and out of the Thermo-Flask. The isopentane bowl was incubated in liquid nitrogen for about 10 minutes. Tissue was completely frozen in approximately one minute, wrapped in aluminum foil, stored immediately in a box containing dry ice, and transferred to a -80°C freezer. Tumor tissues were cryosectioned at -20 degrees onto gene expression slides. RNA-seq: The samples were uniquely barcoded, pooled, and sequenced on HiSeq (Illumina). scRNA-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform aiming for 50,000 reads per cell. scATAC-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform. In total, we generated scATAC-seq profiles from 5,353 cells, which yielded on average 13.0 × 10^3 unique fragments mapping to the nuclear genome. Spatial transcriptomics: The libraries were then sequenced using NextSeq (Illumina). The Gene Expression Slide & Reagent kit was followed per protocol, and used to produce sequencing libraries.