Structural Basis for Cytoplasmic Factors Required for Integrator and CPSF Function
The object of this study (or experiment) was to determine the impact of BRAT1 depletion on the transcriptome during differentiation into neuroprogenitor cells. Two control and two BRAT1 knockout H7-human ESC lines were differentiated for 14 days, total RNA isolated and polyA enriched Click-seq libraries generated. Broad transcriptional misregulation was observed between differentiated knockout and control lines. Specifically, the precocious upregulation of several neurogenesis-driving transcription factors indicates the mistiming of differentiation. Overall design: Samples are human H7 embryonic stem cells (ESCs) that have been ventrally differentiated for 14 days. There are two groups, Day 0 (undifferentiated ESCs) and Day 14 (neural progenitors), with 2 control lines and 2 BRAT1 knockout lines at each. There are three biological replicates of each sample at each condition. MJPro1-3 are three biological replicates of Control Line 1 at Day 14, and MJPro4-6 are Control line 2. MJPro7-9 are three biological replicates of BRAT1 knockout Line 1 at Day 14, and MJPro10-12 are BRAT1 knockout 2 at Day 14. MJPro25-27 are biological replicates of Control line 1 at Day 0, and MJPro28-30 are Control line 2 at Day 0.  Finally, MJPro31-33 are biological replicates of BRAT1 knockout line 1 at Day 0, and MJPro34-36 are BRAT1 knockout line 2 at Day 0.