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 AparicioPublished 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.
Keyphrases
- single cell
- rna seq
- high throughput
- poor prognosis
- gene expression
- papillary thyroid
- transcription factor
- bioinformatics analysis
- genome wide
- squamous cell
- electron transfer
- long non coding rna
- stress induced
- young adults
- dna methylation
- squamous cell carcinoma
- binding protein
- bone marrow
- case control
- childhood cancer