RNA-seq for metaphase II replicate1
For DMS-MaPseq, yeast cultures were treated with 5% DMS for 4 minutes at 30 C. For RNA-seq, cultures were treated with an equal amount of DMSO. The modification reaction was quenched, washed with 30% beta-mercaptoethanol. Total RNA was isolated using hot phenol method and treated with DNase I. Poly(A) mRNA was enriched from 5 g of total RNA through Oligo-dt beads. Further  procedures, including reverse transcription and second-strand synthesis for mutational profiling,  DNA fragmentation, adaptor ligation, USER enzyme digestion, size selection, and PCR amplification, were performed for library generation. Adaptor sequences have been removed, and rRNA reads have been depleted through an alignment against rDNA sequences.