Hsf1_input
250 mL of mid-log growing yeast cells (OD595 = 0.6) were cross-linked with 2% formaldehyde for 30 min at 30oC, the reaction was quenched with glycine (final concentration = 125 mM), and cells were collected by centrifugation. Subsequently, cells were spheroplasted according to the protocol of the Rando lab (Rando, 2010) and then directly sonicated (Bioruptor, Diagenode: ten cycles, 30 sec on/off, medium setting. Cross-links of the input sample were reversed overnight at 65°C in 150 μL 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% SDS. Samples were treated with RNAse and proteinase K, and DNA was recovered for further analysis using phenol extraction. Prior to library preparation the samples were sub-sheared to obtain fragments in the optimal size range (Mokry et al., 2010).