scRNAseq of NT2.5 and NT2.5-LM breast tumors

Syngeneic NT2.5 and NT2.5-LM breast tumors established in female NeuN mice were collected and sent for scRNAseq to examine various cell populations Overall design: For library preparation, 10x Genomics Chromium Single Cell 3' RNA-seq kits v3 were used. Gene expression libraries were prepared per the manufacturer's instructions. 4 biological replicates totaling 8 processed tumors were sequenced in 2 batches: Run A - 2 NT2.5 tumors, 2 NT2.5-LM tumors; Run B - 2 NT2.5 tumors, 2 NT2.5-LM tumors. These tumors were taken as a subset from a larger batch of tumors that include various mouse treatments, with each batch having an equal assortment of samples from multiple treatment groups to reduce technical biases. Here, we restrict our analysis to replicates under the vehicle treatment condition. Illumina HiSeqX Ten or NovaSeq were used to generate total reads. Paired-end reads were processed using CellRanger v3.0.2 and mapped to the mm10 transcriptome with default settings. ScanPy v1.8.1 and Python v3 was used for quality control and basic filtering.