biostudies-literatureTruong DDCory Monzingo FoundationCPRITNIHNIH HHSBlake Abercrombie Foundation488https://www.ebi.ac.uk/biostudies/studies/S-EPMC10230784biostudies-literatureUnknown23(1)<h4>Background</h4>Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas - tumors of mesenchymal origin - are subject to the same technical artifacts, we profiled patient-derived tumor explaBMC cancerDissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing.PMC102307841S10OD024977-01RP180819R01-CA180279-01A1Navin NELazar AJGordon NGorlick RDaw NCLudwig JAKrishnan SGopalakrishnan VLamhamedi-Cherradi SESwaminathan JLivingston JATruong DDPorter RWGibson AfalseDissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing.<h4>Background</h4>Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas - tumors of mesenchymal origin - are subject to the same technical artifacts, we profiled patient-derived tumor expla2023-01-01T00:00:00Z2023 May2025-04-18T17:46:12.634Z2025-04-07T05:21:01.756ZS-EPMC102307843725406910.1186/s12885-023-10977-1