Adipose tissue plasticity in pheochromocytoma patients reveals a key role of the splicing machinery in human adipose browning

RNA-sequencing counts data from omental adipose tissue from control individuals (C1-3) and patients with pheochromocytoma (P1-4) for whole genes (genes-counts.tsv) and individual isoforms (isoform-counts.tsv). Additional details regarding recruited individuals are available in the associated manuscript.

Tissue fragments (~150 mg) of adipose biopsies from controls and pheochromocytoma patients were homogenized using a metal bead-based mechanical procedure in a TissueLyser® (QIAGEN, Düsseldorf, Germany). Total RNA was isolated from tissue homogenates using a NucleoSpin® RNA kit (Macherey-Nagel, Dueren, Germany) following the manufacturer’s protocol. mRNA was purified from 2 μg of total RNA using oligo-dT beads; it was then fragmented, retrotranscribed with random primers, and subjected to second-strand synthesis to create double-stranded cDNA fragments. Adaptor ligation, purification of 200-base pair cDNA fragments, amplification of the purified fragments, and library preparation were performed as previously reported by our laboratory. Before sequencing, the RNA integrity number (RIN) of each sample was determined using an Agilent Bioanalyzer 2100; samples with RIN ≥ 7.5 were used for RNA-sequencing. The cDNA library quality and quantity were further analyzed as previously described. Libraries yielding satisfactory results were sequenced on an Illumina HiSeq 2000 sequencer (DNAvision, Charleroi, Belgium). The average reads per sample was 45 million; this level of coverage was previously shown to provide sufficient sequencing depth for gene expression quantification and transcript detection. Quality control of reads was performed using FastQC (version 0.11.8; bioinformatics.babraham.ac.uk/projects/fastqc). Gene expression was quantified using Salmon version 1.1.0 with the additional parameters “– seqBias – gcBias – validateMappings”. GENCODE version 31 (GRCh38.p12) was used as the reference genome and indexed using default parameters; this resulted in 175,775 transcripts corresponding to 35,183 genes.