Global remodeling of nucleosome positionsing in C. elegans

This website distributes data related to Global remodeling of nucleosome positionsing in C. elegans, Locke et al..

Download Experimental Results

Download mapped reads from the RsaI assay and the HincII assay. All reads are mapped to the WS190 genome. These data are in .wig format. Unmapped reads may be obtained from the Sequence Read Archive under the accession number SRA050182.

We also provide nucleosome occupancy for the RsaI and HincII in vitro assays as well as in vivo occupancy from Gu & Fire and Valouev et al.. (Valouev et al. data have been converted to the WS190 genome as described in the paper.)

• RsaI
• HincII
• Gu & Fire
• Valouev et al.

Download Our Predictions

Below are our predictions on the C. elegans genome

Note that binding energies, probabilities, and occupancies are all predicted on the WS190 genome (with all six chromosomes in one file). These data are presented in .wig format, suitable for display on the UCSC Genome Browser. (These instructions for adding custom tracks explain how to upload the data to the browser.)

Model type

Model types are defined in Locke et al. PNAS 2010

Trained on

The model was trained on this data set. RsaI and HincII are in vitro assays, while Gu & Fire and Valouev et al. are in vivo.

Model parameters

Our fits produce these parameters. See here for instructions on how to use these parameters to predict nucleosome binding energies and occupancies on any genome.

Ranked word-energies

Table ranking the energy contribution of each dinucleotide as predicted by the model. The procedure for producing these tables is described in our paper.

Binding energy

The energy to bind a nucleosome to the genome at a given base-pair (bp).

Binding probability

The probability for a nucleosome to bind at a given bp.

Occupancy

The probability that a nucleosome will cover a given bp. (Occupancy at bp x is the sum of the probabilities from x-146 through x.)