SOX9 is part of a combinatorial marker that reveals early development and embryological origins of the mouse brown adipose tissue depots

Brown adipose tissue (BAT) is a mammalian thermogenic tissue that helps to maintain body temperature and provides other important metabolic functions. Most brown adipocytes are located in structures called depots including the interscapular (iBAT), scapular (sBAT), and cervical (cBAT) depots. BAT depots arise from embryonic structures called somites, but their development is incompletely understood. Here, scRNA-seq was applied to whole-trunk tissue from axial levels where the three major BAT depots are located in order to profile the transcriptome of brown adipocyte progenitors as well as other lineages derived from somites and lateral plate mesoderm. The range of timepoints was chosen to profile brown adipocyte progenitors from early lineage segregation, as observed by a combination of markers including Sox9 at E11.5, to E13.5 when depots are morphologically identifiable and brown pre-adipocyte markers are expressed. Whole trunk tissues from mouse embryos were manually dissected to include C3-T2, or the third cervical to the second thoracic segments at three different embryonic stages (E11.5, E12.5, E13.5). Three littermate replicates were pooled together for each sample. Briefly, trunks were excised at the axial levels indicated and the thoracic organs and forelimbs were removed. Remaining tissue includes the trunk (both somite and lateral plate mesoderm derivatives) and neural tube.