title: GSM6756784: SX3627; Caenorhabditis elegans; RNA-Seq
library_construction_protocol: In vivo MNAse digestion was performed on purified nuclei isolated from C. elegans (WT, swsn-1-/-, swsn-1-/-; snfc-5-/-, swsn-1-/-; snfc-5-/-; ubr-5-/-) L1 frozen popcorns. Frozen popcorns containing ~60,000 L1s for each strain was individually homogenized in liquid nitrogen and purification was optimised using sigma nuclei pure prep nuclei isolation kit (NUC-201) with modifications. Purified Nuclei of 500 ng/reaction were digested with MNAse (M0247S, NEB) concentration 200U/ml or 250U/ml for 15 mins at 37 °C to generate monoucleosomal DNA. MNase digestion was terminated by adding stop solution containing 3% SDS, 20 mM EDTA. Mononuclesomes were treated with Proteinase K (Invitrogen) and incubated at 65°C for 1 hr followed by DNA purification using Zymo clean and Concentrator. Mononucleosome bands were confirmed by D5000 ScreenTape in Agilent 2200 TapeStation system. For library preparation, DNA was measured again with Qubit dsDNA HS Assay Kit and 65 ng of mononucleosomal purified DNA was used for NEBNext Ultra II DNA Library Prep Kit for Illumina with size selection. DNA libraries were prepared for sequencing using NEBNext Ultra II DNA Library Prep Kit for Illumina