library_construction_protocol: RNAs were extracted from isolated cells using the RNeasy Mini kit (Qiagen). Sequencing libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina). Samples were sequenced 50 bp paired-ended at 10 million to 20 million reads per replicate on an Illumina HiSeq. 2500 instrument. Library preparation and sequencing were performed at New York University School of Medicine Genome Technology Center. All the reads were mapped to the mouse reference genome (mm10) using the STAR aligner (v2.5.0c)69. Alignments were guided by a Gene Transfer File (GTF, version GRCm38.74) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard/). The read count tables were generated using HTSeq (v0.6.0)70and normalized based on their library size factors using DESeq. 2 (v3.0)71 and differential expression analysis was performed. The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0)72 and bedGraphToBigWig tool (v4), and downstream statistical analyses and generating plots were performed in R environment (v3.1.1) (http://www.r-project.org/).