scRNA-Seq and snATAC-Seq of CNC and SHF lineage traced Mouse Aorta

Lineage-tagged experimental mice were generated by crossing Wnt1-Cre (CNC lineage traced) or Mef2c-Cre (SHF lineage traced) mice with YFP mice. Fourteen-week-old male mice were used for scRNA-Seq and snATAC-Seq studies. Aortic tissues were collected from anesthetized mice, excised, and digested with an enzymatic cocktail. scRNA-Seq samples contain 2 pooled mouse aortas, and scATAC-Seq samples contain 5 pooled mouse aortas. Cells were stained for viability and sorted based on YFP fluorescence. YFP+ samples are lineage positive and YFP- samples are lineage negative. For single-cell RNA sequencing, separate single cell libraries were created from YFP+ and YFP- cells using the 10X Chromium Next GEM Single Cell 3' Kit v3.1. A single library was sequenced using the NextSeq 550 system (75 cycles) and 7 libraries were sequenced on the Illumina NovaSeq S1 system (100 cycles). Demultiplexing and alignment were performed using Cell Ranger (v6.1.2) on the 10X cloud. Sequenced reads were aligned to a custom genome containing the 10X genomics mm10 genome with the addition of our YFP gene sequence. For single-nucleus ATAC sequencing, only YFP+ sorted cells were used to create libraries. 4 Libraries were prepared using the 10X Chromium Next GEM Single Cell ATAC Reagent Kit v2, and sequenced on the Illumina NextSeq 2000 system. Demultiplexing and alignment were performed using Cell Ranger ATAC (v1.2.0) on the HYAK supercomputer at UW. Sequenced reads were aligned to the 10X genomics mm10 genome.