Nucleosome Track Settings
 
Nucleosome predictions from SOLiD Core Alignments   (All Mapping and Sequencing tracks)

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 Control  mononucleosome control   Schema 
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 fragments +  mononucleosomal fragments, sense strand reads   Schema 
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 fragments -  mononucleosomal fragments, antisense strand reads   Schema 
Data coordinates converted via liftOver from: Jan. 2007 (WS170/ce4)

Description

Mononucleosome control track

The control data was produced from the lightly micrococcal nuclease-digested paired-end sequenced genomic DNA fragments in the size range of 400-900 base pairs. Each feature corresponds to one end of the paired-end fragment with thick portion representing the sequenced 25 base pairs of that end. Features span 147 base pairs (displayed equivalently to mononucleosome data).

Mononucleosome sense strand reads

Mononucleosomal fragments were obtained by micrococcal nuclease digestion of C. elegans lysates, DNA extraction, and sequencing of nucleosome-bound DNA fragments. Features represent inferred 147 base pair cores from fragments that mapped to the sense strand of the reference genome. The thick portion of each feature (50 base pairs) represents the sequenced part of the nucleosome-bound fragment.

Mononucleosome antisense strand reads

Mononucleosomal fragments were obtained by micrococcal nuclease digestion of C. elegans lysates, DNA extraction and sequencing of nucleosome-bound DNA fragments. Features represent inferred 147 base pair cores from fragments that mapped to the antisense strands. The thick portion of each feature (50 base pairs) represents the sequenced part of the core.

Display Conventions and Configuration

In each of the sub-tracks, sequences starting at the same base pair were collapsed and color-coded from the lightest to the darkest color in five shades according to the following category-based scale:

Number of read instancesColor shade
1lightest
2light
3-5medium
6-10dark
more than 10darkest

Hold your mouse over individual items in each track to see the number of read instances starting at that base pair.

Credits

The data for this track is supplied by the Sidow Lab and the Fire Lab at the Stanford School of Medicine.
Track display advice provided by Hiram Clawson, UCSC Genome Browser Engineering.

References

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. PMID: 18477713; PMC: PMC2493394

Supported oligo ligation detection (SOLiD) sequencing technology from Applied Biosystems.