PolyA-tail enriched RNA-seq in differentiating TX1072 XX mESCs

Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use polyA-tail enriched RNA-seq within the wildtype TX1072 XX cell line after two days of differentiation. RNA-seq enriched for polyadenylated fragments was performed in differentiating TX1072 XX mESCs using the TruSeq RNA Sample Preparation Kit v2 (Illumina).