Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing.
Danh D TruongSalah-Eddine Lamhamedi-CherradiRobert W PorterSandhya KrishnanJyothishmathi SwaminathanAmber GibsonAlexander J LazarJ Andrew LivingstonVidya GopalakrishnanNancy GordonNajat C DawNicholas E NavinRichard GorlickJoseph A LudwigPublished in: BMC cancer (2023)
We highlighted transcriptional biases, including warm dissociation and gene-length biases, introduced by the dissociation method for various sarcoma subtypes. This work is the first to characterize how the dissociation methods used for sc/snRNA-seq may affect the interpretation of the molecular features in sarcoma PDXs.