Single-cell gene expression profiling of SOXC-mutant bone and bone marrow cells

SOXC genes (i.e., SOX4, SOX11 and SOX12) encode for transcription factors controlling survival, proliferation, commitment and differentiation of several cell types from development onwards. Although human diseases indicate crucial roles for SOXC in bone development and maintenance, SOXC activities in osteoblastic cells remain elusive. Here, we used a mouse model to inactivate SOXC genes in the osteoblast lineage cells using an OsxCre transgene (Sox4fl/fl Sox11fl/fl Sox12fl/fl OsxCre mice referred to as SOXCOsxCre mice) and we used single-cell RNA-sequencing assays to characterize gene expression changes in bone and bone marrow cells in adulthood. Femurs and tibiae were collected from 7- and 13-week-old female SOXCOsxCre and control mice (2 mice per genotype and age). After periosteum removal and bone marrow flushing, bones were digested with LiberaseTM and EDTA to release bone and endosteal bone marrow cells. Hematopoietic cells were removed by immunomagnetic sorting, while remaining cells were used for scRNA-seq analysis.