title: GSM5551631: Hinput_E12_ftag_EMX2_neg1; Mus musculus; ChIP-Seq
library_construction_protocol: Nuclear extracts were prepared from sorted cells and digested with MNase to obtain mono- and di-nucleotide fragments. Digested chromatin was dialysed overnight. Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against H3K27ac (Abcam, ab472) or H3K27me3 (Active motif, 39157). Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction. Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina). Nuclear extracts were prepared from  cells and sheared using a bioruptor (18-40 cylces; 30s ON and 45s OFF). Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against the relevant TF or IgG or a blocking peptide overnight at 4C.  Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction. Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina).