Analysis of gene expression patterns in brown adipose tissue

Brown adipose tissue is a specialized fat tissue involved in heat generation by using a process termed thermogenesis. This ability to convert nutrient energy into heat sets brown adipocytes apart from the more common type of white adipocytes, which are mainly involved in energy storage. Brown adipose depots occur as a large interscapular depot in mice. Brown adipocytes are multilocular, i.e. contain many small lipid-filled vacuoles and uniquely express the uncoupling protein 1. In this study, the gene expression patterns in brown adipose tissue samples of young, healthy mice was analyzed. Male C57Bl6J mice were housed under controlled conditions at 22 ±2 °C in an 12/12-hour light/dark cycle maintained on a standard chow diet (Ssniff, Soest, Germany). The animals were killed at 10 weeks of age by cervical dislocation. Brown adipose tissue depots were isolated and immediately frozen in liquid nitrogen. RNA was isolated from 50 mg of tissue. NGS sequencing was conducted using Illumina HiSeq 2000 with 2 x 100 bp reads (LGC genomics, Berlin, Germany). For data processing and analysis, FASTQC v0.11.8 was used for quality assessment and trimmgalore v0.6.4 was applied for filtering adapter sequences and small reads. The clean reads were mapped to a reference genome (Genome Reference Consortium Mouse Build 38 mm10) using the alignment tools HISAT2 v2.1.0 and Bowtie2 v2.3.5.1 Expression levels were quantified Cufflinks v.2.2.1.