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 instances | Color shade |
| 1 | lightest |
| 2 | light |
| 3-5 | medium |
| 6-10 | dark |
| more than 10 | darkest |
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, Sidow A, Fire A, Johnson SM.
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. Epub 2008 May 13.
Supported oligo ligation detection (SOLiD) sequencing technology from
Applied Biosystems.