Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation

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A single-cell RNA sequencing experiment was conducted using 10x Genomics technology on samples from three distinct groups, which included six bones, meninges, and the brain. The study comprised three groups: those that underwent MCAo surgery, those that underwent sham surgery, and a group of naive animals. Each sample consisted of cells pooled from three animals, with a total of 32 samples utilized. The MCAo surgery group contributed 2 samples, each consisting of cells pooled from 3 different animals. The sham and naive groups served as control groups. In addition to the single-cell RNA sequencing, bulk RNA sequencing experiments were conducted using the Illumina ligation stranded mRNA preparation kit. These experiments involved samples from the six bones under the three conditions (naive, sham, and MCAo). Separate measurements were taken for 4-6 animals per condition, yielding a total of 95 samples. Furthermore, bulk RNA sequencing was carried out using Smart-seq2 for mini-bulks of about 50 CD45+/Cd11b+ sorted immune cells each from the skull and femur. These samples were taken from wildtype animals (5 in total) and 5xFAD animals (3 in total), amassing 168 samples overall, with approximately 20 samples per animal.