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Genome-Wide Predictions
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Raw Data

Raw data is available at GEO under accession number GSE13622.

Normalized nucleosome occupancy

We extended the mapped nucleosome reads of each experiment to the average nucleosome length in that experiment (always between 140-170bp). For each map, we then calculated at every basepair the log-ratio between the number of reads that cover that basepair and the average number of reads per basepair across the genome. We then set the genomic mean in each sample to zero by subtracting the genome-wide mean from every basepair. Finally, we averaged the replicates within each experimental condition, resulting in four tracks of log-normalized nucleosome occupancy. For data visualization purposes, we also provide the four tracks without the log and zero transform.

 Normalized nucleosome occupancyNucleosome occupancy (without log)
In Vitro

Downlaod genomica project file and view the above tracks in Genomica Genome Browser project file (requires 300MB of RAM):     (28MB), Download Genomica here.

The above tracks are in a tab delimited file (.chv) where each row consists of the following columns:
ChromosomeRegion startRegion endValues list (delimited by semicolon)

Note that the genomic coordinates are 1-based.

We supply a perl script named that converts the .chv file to a more standard format:

In order to convert a file to the more standard format, first unzip it, then run the script on it: <chv input file name> -o <output file name>

Synthetic Oligonucleotides

We created a pool of ~40,000 double-stranded oligonucleotides of length 150bp, each flanked by common priming sites, and combined the pool with limiting amounts of chicken histones to form nucleosomes. DNAs in reconstituted nucleosomes were separated from unincorporated DNAs by native gel electrophoresis, without the use of any micrococcal nuclease. We then extracted from the gel the DNA that had successfully competed to form nucleosomes, and used both parallel sequencing and microarrays to compare the nucleosomal DNAs to DNAs in the initial pool. For each sequence, we calculated the log-ratio between the reconstituted fraction and the initial pool as a measure of the nucleosome affinity of that sequence. In the sequencing results, we use oligonucleotides that were sequenced at least once and at most 500 times in each experiment.
Synthetic oligonucleotides measured by microarray:
Synthetic oligonucleotides measured by sequencing: