title: GSM2445192: HiC BMDN replicate 1 PCR replicate 1; Mus musculus; OTHER
library_construction_protocol: The in-situ Hi-C experiments were performed similarly as described (Rao SSP, et al. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159: 1665-1680). The GRO-Seq experiments were performed as described (Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-8). The ChIP-Seq experiments were performed similarly as described (Lin YC, et al. 2012. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol 13: 1196-1204). The MeDIP-Seq experiments were performed similarly as described (Pomraning KR, Smith KM, Freitag M. 2009. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47: 142-150). For RNA-Seq: total RNA was isolated using RNeasy Mini kit (Qiagen). RNA was treated with TURBO DNase (Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA purification kit (Life Technologies).cDNA was generated with the First-strand synthesis kit (Life Technologies) using a combination of random hexamers and oligo(dT) in presence of actinomycin D. Second-strand synthesis was performed with dUTP instead of dTTP. The ds-cDNA was sonicated to 200-400 bp using the S220 Focused-ultrasonicator (Covaris). Hi-C libraries were prepared with the NEBNext primer set and were selected by size by 6% PAGE and sequenced for 50 cycles on Illumina HiSeq 2500. GRO-Seq libraries were prepared with custom GRO-Seq PCR primers and were selected by size by 8% PAGE and sequenced for 50 cycles on Illumina HiSeq 2000. ChIP-Seq and MeDIP-Seq libraries were prepared with the NEBNext primer set and were selected by size by 8% PAGE and sequenced for 50 cycles on Illumina HiSeq 2000 or 2500. RNA-Seq ibraries were prepared with the TruSeq primer set and were selected by size by 8% PAGE and sequenced for 50 cycles on Illumina HiSeq 2000.