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Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses.

Ciara H O'FlanaganKieran R CampbellAllen W ZhangFarhia KabeerJamie L P LimJustina BielePeter EirewDaniel LaiAndrew McPhersonEsther KongCherie BatesKelly BorkowskiMatt WiensBrittany HewitsonJames HopkinsJenifer PhamNicholas CegliaRichard MooreAndrew J MungallJessica N McAlpinenull nullSohrab P ShahSamuel A J R Aparicio
Published in: Genome biology (2019)
The method and conditions of tumor dissociation influence cell yield and transcriptome state and are both tissue- and cell-type dependent. Interpretation of stress pathway expression differences in cancer single-cell studies, including components of surface immune recognition such as MHC class I, may be especially confounded. We define a core set of 512 genes that can assist with the identification of such effects in dissociated scRNA-seq experiments.
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