library_construction_protocol: cells were resuspended in 1XPBS and crosslinked with 1% formaldehyde for 10 min at room temperature. The formaldehyde was quenched with addition of 0.125M glycine, washed three times with PBS-0.05% tween-20, and cell pellets were snap freeze in liquid nitrogen for CHART experiment as previously published with biotenylated 7SL sense or antisense probes After CHART, libraries were constFor each sample 2pg of drosophila S2 cells sonicated DNA was spike-in. sequencing libraries were than prepared with NEBNext® Ultra II DNA Library Prep Kit for Illumina