Fig. 1
From: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq
Overview of the setup to study dynamics of gene silencing on the Xi during XCI. Female ES_Tsix-stop ESCs [39] display non-random XCI due to a transcriptional stop in the coding region of Tsix, allowing allele-specific quantification of transcripts originating from the (future) Xi by RNA-seq (pink background). To investigate stable XCI from the same female ES_Tsix-stop ESCs, we performed RNA-seq on a clonal NPC line derived from the ES_Tsix-stop ESCs (*NPC_129-Xi, red background) [35]. Also, we included RNA-seq on two NPC lines generated from the F1 hybrid ESCs before introduction of the transcriptional Tsix stop. Clonal lines were generated from these two NPC lines to ensure complete XCI skewing towards inactivation of the M.m. castaneus (Cast)- or the M.m. musculus (129)-derived X chromosome (NPC_Cast-Xi, orange background and NPC_129-Xi, dark purple background, respectively) [35]