title: GSM4478260: in vitro_WT_H3K4me3; Mus musculus; ChIP-Seq
library_construction_protocol: The nucleosome was extracted using TruChip Chromatin Shearing Reagent Kit (Covaris, 520127). DNA was sheared using Covaris E220/S220 for 20 min in cold circulating water. ChIP was done using the ChIP-IT high sensitivity kit (Active Motif, 53040). For all the rest of the ChIP-seq experiments, which are Mnase based native ChIP, nuclei are extracted using NP40 detergent at the final concentration of 0.6%. The Di-nucleosomes and mono-nucleosomes are generated by enzymatic digestion using diluted MNase. for H3.3 ChIP-seq in cocultured LKS cells, DNA was eluted and library was prepared using ThruPLEX DNA-seq Kit Dual Index (Rubicon Genomics, R400523). For all the rest of the ChIP-seq experiments, DNA library was prepared using Kapa Hyper Kit (KK8504) according to the product manual. Adaptor was from KAPA Single-Indexted Adaptor Kit (KAPA 8700 08005699001). DNA was purified using the DNA purification kit AMPure XP 60 mL (A63800, Beckman Coulter). 13 cycles of PCR amplication cycles are used.
attributes.tag: GEO Accession
attributes.value: GSM4478260