title: GSM4878799: ChIP_ESC_Ola_Input_CST_IFNb_1h_Rep5; Mus musculus; ChIP-Seq
library_construction_protocol: ATAC-seq: . For ESCs, the cell pellet was resuspended in 200 µl ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl2, 3 mM MgCl2, 0.1 % NP-40) and incubate for at room temperature for 2 min. 20 µl ATAC reaction buffer containing 10 µl 2x transposase buffer and 2.5 µl Tn5 enzyme (Illumina) was added and samples were incubated at 37 °C for 30 min. Samples were purified. For MEFs, the lysis buffer contained additionally 1 % digitonin. ATAC-seq: Purified samples were directly amplifed, barcoded and purified. ChIP-seq for histone marks in ESC: Cells were crosslinked by 1 % Formaldehyde for 10 min at room temperature and stopped with 125 mM Glycine for 5 min. Samples of around 40 million cells were treated with 40 U of MNase for 15 min at 37 °C. The samples were shared for 15 min (Burst 200; Cycle 20%; Intensity 8). Replicate 1 was shared for 30 min and no MNase treatment was performed. 4µg of antibody was used per sample and incubated for 2 hours at 4 °C. Protein G-beads were added over night. Multiple low and high salt washes were performed and the samples were eluted. Samples were reverse crosslinked and stored at -20°C. ChIP-seq for histone marks in ESCs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) ChIP-seq for STATs in ESCs and MEFs: The isolation of the chromatin was done with Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003) ChIP-seq for STATs in ESCs and MEFs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) RNA-seq: Total RNA was isolated using NucleoSpin RNA Plus Kit (Macherey-Nagel, 740984.250). Depletion of rRNA was done with Ribo-Zero rRNA Removal Kit (Illumina, 15066012) for ESCs and MEFs and with NEBNext® rRNA Depletion Kit (New England Biolabs, E6350). RNA-seq: Libraries were prepared using NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina (New England Biolabs, E7760). scATAC-seq: The experiment was performed based on the standard manufacturer's protocol Chromium Single Cell ATAC Reagent Kits (PN-1000110). scRNA-seq: The experiment was performed based on the standard manufacturer's protocol of Chromium Single Cell 3' Reagent Kits v2 (PN-120237).