September 11, 2025 Dataset Open Access

Integrated Seurat data object from single-nucleus mRNA-sequencing of brown adipose tissue of mice in response to cold exposure

Adlung, Lorenz

Researcher(s)

This Seurat object (v5.1) contains single-nucleus RNA-sequencing data from murine interscapular brown adipose tissue (BAT). The dataset comprises 36,611 nuclei from six samples representing two genotypes (ChREBP^flox/flox^ Ucp1-Cre negative [Cre-] and Ucp1-Cre positive [Cre+]) across three housing conditions: room temperature (22°C, RT), acute cold exposure (24 hours at 6°C, AC), and chronic cold exposure (10 days at 6°C, CC). BAT from 3-4 male mice (12-20 weeks old) was pooled per sample. Libraries were prepared using the 10X Genomics Chromium Single Cell V3.1 reagent kit and sequenced on an Illumina NovaSeq platform with paired-end 150 bp reads, targeting approximately 50,000 read pairs per nucleus.

Raw sequencing data were processed using Cell Ranger (v7.1.0) with alignment to the GRCm38 (mm10) reference genome. Quality control filtering excluded nuclei with >15% mitochondrial reads, >25,000 UMI counts, or >5,000 detected genes, as well as genes detected in fewer than 3 cells. The six samples were integrated using the Harmony algorithm (v1.2.3). Clustering was performed using the top 30 principal components at resolution 0.8, yielding 21 annotated cell populations: seven adipocyte subtypes (basal brown, OXPHOS-high brown, white-like, lipogenic brown, endothelium-derived brown, stroma-derived brown, and contractile brown adipocytes), three stromal cell types, three endothelial cell types (capillary, arterial, venous), two muscle fiber types (fast and slow), myeloid cells (MonDC), smooth muscle cells, pericytes, lymphocytes, satellite glia cells, and Schwann cells. Key metadata columns include sample identifier (orig.ident), genotype, housing condition, cluster assignments (seurat_clusters), annotated cell type names (cell_type), and DoubletFinder classifications.