For Hi-C, cells were fixed with 1% formaldehyde for 10 minutes at room temperture, quenched with 0.2M Glycine for 5 minutes. Adherent cells were fixed on the tissue culture plate and removed using a cell scraper. Suspension cells were fixed in suspension. After fixation and quenching, cells were pelleted, washed 1X with DPBS, pelleted again, and frozen on dry ice. Samples were stored in -80C until further processing. For RNA, cells were harvested in Trizol according to the manufacturers instrutions. After homogenization, samples were stored at -80C until further processing. RNA was isolate using the Purelink RNA mini kit with on column Dnase I treatment. RNA integrity was evaluated using RNA tapestation. In situ Hi-C was performed accoring to Rao et al. Cell 2014 using the MboI restriction enzyme. Libraries were sequenced on the NextSeq 500 platform. Stranded mRNA-seq libraries were constructed using the Illumina stranded mRNA seq kit according to the manufacturers instructions. Libaries were sequenced on the NextSeq 500 platform. MboI in situ Hi-C Stranded mRNA-seq