Library preparation for mRNA sequencing was performed as previously described (43). Library preparation for ChIRP sequencing was performed according to the NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs). Libraries were tested for quality and quantified using a NanoDrop 2000 (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies). Single-end 50–base pair (bp) sequencing data were generated on an Illumina HiSeq2000 using Illumina TruSeq SBS kits.

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