GSM9487825: scRNA-seq of multiplexed dissociated tumor tissues (BAP1 WT/KO; subcutaneous and ocular Melan-a models); Mus musculus; RNA-Seq
For bulk RNA-seq, total RNA was extracted from cultured cells using a column-based RNA isolation kit following the manufacturer's instructions, including on-column DNase treatment. For whole-genome and whole-exome sequencing, genomic DNA was extracted using a standard phenol–chloroform or silica column–based method. For single-cell RNA sequencing, freshly isolated or fixed tumor tissues were mechanically and enzymatically dissociated into single-cell suspensions prior to library preparation according to the 10x Genomics fixed tissue workflow. Bulk RNA-seq libraries were prepared from polyadenylated RNA using a stranded mRNA library preparation kit. Whole-genome sequencing libraries were prepared from genomic DNA using a PCR-free or low-cycle library preparation protocol. Whole-exome sequencing libraries were generated using a hybrid-capture–based exome enrichment kit. Single-cell RNA-seq libraries were constructed using the 10x Genomics Chromium platform following the manufacturer's protocol for fixed tissue gene expression, generating barcoded single-cell cDNA libraries.