Newly synthesized RNA analysis in WT, SAGA and ATAC mutant mouse embryonic stem cells

To analyse the genome-wide impact of inactivation of the ATAC or SAGA coactivator complexes on RNA polymerase II (Pol II) transcription, we purified newly synthesized RNA from mutant mouse embryonic stem (ES) cell lines in which subunits of ATAC (Yeats2, Zzz3) or SAGA (Supt7l) are inactivated or depleted. We also performed this analysis in mutant cell lines in which a subunit (Tada3) of the shared histone acetyltransferase activity of these two complexes is depleted. Newly synthesized RNA was purified following the 4sU labelling method (more details in extract protocol). For two wildtype samples, the total RNA input was also analysed. Overall design: Total and newly synthesized RNA from wildtype (WT) and mutant mouse ES E14 cell lines. Samples were sequenced in three independent sequencing projects over the course of three years (project 1: VQFR1-12, project 2: VQFR13-18, project 3: VQFR25-28) RNA from two independent clones per cell line were sequenced.