Transcriptomic analysis of the effect of LINE-1 silencing on E14 mouse cortex in vivo

Mouse brain cortices at embryonic day 12 (E12) were in utero electroporated with a plasmid expressing a short hairpin RNA against LINE-1s (shL1), or with a control shRNA (shCtrl). A plasmid expressing GFP was co-electroporated with the ones containing shRNAs.At E14, GFP+ cells from shControl, or shL1, samples were FACS-sorted in n=3 pools of 200 cells each for direct RNA-Seq library preparation using the SMART-Seq HT PLUS kit (Takara). RNA-Seq libraries from FACS-sorted GFP+ cells were sequenced in paired-end mode (2x50bp).