title: GSM3332090: RNA-Seq_Smc1-6HA_Biological replica 1; Saccharomyces cerevisiae; RNA-Seq
library_construction_protocol: Total RNA was extracted using Qiagen RNeasy Protect Kit. Total RNA was depleted for ribosomal RNA using Ribo-Zero Magnetic Kit (Illumina) Libraries of mononucleosomal and ChIP DNA were constructed following the Illumina compatible NEXTflexTM ChIP-Seq kit protocol and sequenced in an Illumina NextSeq500 platform using the paired-end protocol. Reads were aligned to the S.cerevisiae (SacCer3) genome using Bowtie. Nucleosome occupancy maps were generated using the NUCwave algorithm.  Nucleosome fuzziness was analyzed using the dpos utility of DANPOS2 application. To make it compatible with NUCwave maps, we used the following parameters: a span of 1 bp and a read extension of 50 bp. ChIP-seq data representation was performed using the Model-based Analysis of ChIP-Seq (MACS) with a read extension of 147 bp.