GSM8330139: DMB006_gRNA10_rep3_batch2; Homo sapiens; RNA-Seq
For RNA-seq in Group 4 MB PDX, freshly isolated DMB006 cells from mouse brains were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 90% of cells were infected. Cells were cultured for 7 days and then collected for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing. For RNA-seq in D283, cells were infected in triplicate with non-targeting control or KDM2B gRNA viruses at high MOI to ensure more than 80% of cells were infected. Cells were cultured for 7 days. An aliquot of cells was collected on day 4 or day 7 for RNA-seq. Infection efficiency was determined by flow cytometry analysis of GFP percentage on day 4. Editing efficiency was evaluated by targeted deep sequencing. RNA extraction was performed using RNeasy Plus kit (Qiagen) according to manufacturer's instructions. RNA libraries for RNA-seq were prepared following manufacturer's protocols