normalization data transformation protocol
The entire length of the sequenced tags were aligned to the reference genome using Corona Lite software provided by the SOLiD system, allowing up to three mismatches. This process was repeated for the remaining tags, after removal of the 3? most 6 bp, which tend to have higher error rates For Peak calling GeneTrack algorithm was used with fine-grain smoothing (s5, e=10) Singleton peaks were filtered out. Singletons are defined as peaks wherein all associated reads are located at a single chromosomal coordinate. Peak-pairing is performed individually for each locus rather than a global shift of tags on each strand, which is intended to maximize the resolution for bound locations. Peakpairs are matched based on the genome-wide mode for all possible peak-pairs for a given data set.Default Parameters:Upstream peak-pairing limit: u=0, Downstream peak-pairing limit: d = 80, Bin size (bp): b=2, Peak-pairing method: m=mode Genome_build: s288c R64-1-1 Supplementary_files_format_and_content: The Detailed (D_) output reports the peak interval for each peak within a peak-pair, as well as the peak pair midpoint coordinate, the sum of the tags and peak pair distance. Supplementary_files_format_and_content: A peak pair is the matching of a peak on one strand with a peak on the opposite strand within the limits set by parameters listed in the file name. Typically the genomic coordinate that is midway between a peak-pair is either the point of crosslinking or the center of its binding location.
Cells were grown in YP+2% palatinose till the OD600=0,4. Approx. 10*8 cells were taken for each sample
nucleic acid library construction protocol
Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. Libraries were prepared by Peconic Gemomics according to standart ChIP-exo protocol (Rhee, H.S., and Pugh, B.F. (2012). ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr. Protoc. Mol. Biol. Chapter 21, Unit 21.24.).
sample treatment protocol
Cells were lysed according to standart ChIP-exo protocol (Rhee, H.S., and Pugh, B.F. (2012). ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr. Protoc. Mol. Biol. Chapter 21, Unit 21.24.).