Transcriptomic analysis of shCtrl and shCTCL organoids by bulk RNA-seq. Transcriptomic analysis of shCtrl and shCTCL organoids by bulk RNA-seq

To explore the mechanism for the role of CTCLduring cortical development, we compaired the transcriptomes of shCtrl and shCTCL organoids by bulk sequencing Overall design: Stable line of shCtrl and shCTCL were generated by transfecting Human ES line H9 with lentivirus. Then, ES cells were processed organoid culture protocal. At day30, RNA from 2-4 organoids of each group were purified with the HiPure Total RNA Mini Kit. Raw reads were mapped to the hg19 reference using Hisat2 software, then transcripts were measured with StringTie/prepDE.py and differentially expressed genes were identified using R package Ballgown.