GSM4647448: Set2 ChIP-seq, input DNA: Spn1-AID + DMSO 1; Saccharomyces cerevisiae; ChIP-Seq
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 1 mg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding an HA-tagged protein (FWP568) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. Five percent (40 μL) was set aside as input and stored for later processing. The saved input was thawed from storage, and 60 μL LB140 and 100 μL TES were added. The 200 μL of input was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119). Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.