Biological and genetic characterization of a newly established human external auditory carcinoma cell line, SCEACono2

Squamous cell carcinoma of the external auditory canal (EACSCC) is an extraordinarily rare and aggressive malignant disease. Establishment of EACSCC cell line with robust molecular characteristics is essential for the basic and translational research of EACSCC. In this study, we showed the newly established EACSCC cell line SCEACono2, derived from a patient with well-to-moderately differentiated EACSCC. To elucidate the transctomic features of SCEACono2, we performed RNA-seq and revealed its unique characteristics and compared with publicly available head and neck squamous cell caricnoma (HNSCC)-derived cell lines HSC4 and SCC9. Overall design: Library preparation from RNA extracted from cultured cells and RNA sequencing were performed using a DNBSEQ-G400 sequencer at the Beijing Genomics Institute (Shenzhen, China). The sequenced reads were aligned to the human reference genome GRCh38 using STAR v2.7.9a with Gencode v38 annotations. Gene count tables were generated with RSEM v1.3.1.