Two opposing gene expression patterns within ATRX aberrant neuroblastoma
To study the role of distinct ATRX aberrations in neuroblastoma we created isogenic ATRX aberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid. We created ATRX knock-out models, ATRX in-frame exon 2-10 deletions and ATRX in-frame exon 2-13 deletions. Additionally, we included patient-derived models data (i.e. cell line data and one tumoroid). Overall design: We performed gene expression profiling analysis using data obtained from total RNA-sequencing. We compared each of the distinct ATRX aberrant isogenic models with the corresponding wild-type clones. Additionally, we compared the patient-derived ATRX aberrant models with the patient-derived ATRX wild-type models (i.e. CHLA-90+SKNMM+AMC772T2 versus GIMEN+SKNAS+SKNSH+LAN6+SJNB12; patient-derived model data except AMC772T2 is available at ENA accession number PRJEB55331). ** The submitter states that the raw data for the patient-derived tumoroid samples cannot be shared due to patient confidentiality concerns**