hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export I

To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using rRNA-depleted RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs. Overall design: rRNA-depleted RNAs isolated from nuclei of control, hRRP40 or hMTR4 siRNA treated HeLa cells were generated by deep sequencing, using Illumina HiSeq 2000.