This track is produced as part of the ENCODE Transcriptome Project.
Transcription of different
RNA extracts from different
sub-cellular localizations in different
is compared in companion experiments using three different technologies:
tiling arrays, RNA-seq using Solexa, and RNA-seq using SOLiD. The
tiling array data are shown in this track.
The Raw Signal view shows an estimate of abundance of RNA molecules
and the Transfrags view
shows the locations of sites corresponding to these molecules.
Display Conventions and Configuration
To show only selected subtracks, uncheck the boxes next to the tracks that
you wish to hide.
Color differences among the views are arbitrary. They provide a
visual cue for
distinguishing between the different cell types and compartments.
Regions with negative signal value are areas
where the mismatch probe hybridizes better than the match probe.
This could indicate presence of a SNP, a site of RNA editing, or
- The Transfrags view includes all transfrags before filtering.
- Filtered Transfrags
- The Filtered Transfrags view excludes repeats and other known annotations
tRNAs and rRNAs, mi/snoRNAs, things mapping to the mitochondrial or Y
and many predicted snoRNAs and miRNAs.
- Raw Signal
- The Raw Signal view shows the probe intensity based on all probes.
- Filtered Signal
- The Filtered Signal view shows the probe intensity based on the
filtered set of probes.
Cells were grown according to the approved
ENCODE cell culture protocols.
RNA molecules longer than 200 nt
and present in RNA population isolated from different subcellular compartments
(such as cytosol, nucleus, polysomes and others) were fractionated into polyA+
and polyA- fractions as described in
Each RNA fraction was converted into double-stranded cDNA using
labeled and hybridized to a tiling 91-array set containing probes against the
portion of the human genome tiled on average every 5 bp (center-to-center of
each consecutive 25-mers).
All arrays were scaled to a median array intensity of 330. Within a sliding
61 bp window
centered on each probe, an estimate of RNA abundance (signal; see the
Raw Signal view)
was found by calculating the median of all pairwise average PM-MM values,
where PM is a
perfect match and MM is a mismatch. Kapranov et al. (2002), Cheng
et al. (2005) , Kapranov et al. (2007), and Cawley
et al. (2004)
are good references for the experimental methods. Cawley et al.
also describes the analytical methods.
The reproducibility of the labeling method was assessed separately. Three
technical replicates were generated from the same RNA pool for each RNA
hybridized to duplicate arrays (two technical replicates) that contain the
Labeled RNA samples were then pooled and hybridized to the tiling 91-array
the whole genome. Transcribed regions (transfrags; see the Transfrags
generated from the Raw Signal by merging genomic positions to which
are mapped. This merging was based on a 5% false positive rate cutoff in
bacterial controls, a maximum gap (MaxGap) of 40 base-pairs and minimum run
of 40 base-pairs.
These data were generated and analyzed by the transcriptome group at
and Cold Spring Harbor Laboratories:
P. Kapranov, I. Bell, E. Dumais,
J. Drenkow, J. Dumais, N. Garg, M. Lubinsky,
Carrie A. Davis, Huaien Wang, Kimberly Bell, Jorg Drenkow, Chris Zaleski,
and Thomas R. Gingeras.
edu (Tom Gingeras)
Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D,
Piccolboni A, Sementchenko V, Cheng J, Williams AJ et al.
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.
Cell. 2004 Feb 20;116(4):499-509.
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J,
Stern D, Tammana H, Helt G et al.
Transcriptional Maps of 10 Human Chromosomes at 5 Nucleotide Resolution.
Science. 2005 May 20;308(5725):1149-1154.
Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP,
Large-scale transcriptional activity in chromosomes 21 and 22.
Science. 2002 May 3;296(5569):916-9.
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT,
Stadler PF, Hertel J, Hackermüller J, Hofacker IL, et al.
RNA maps reveal new RNA classes and a possible function for pervasive transcription.
Science. 2007 Jun 8;316(5830):1484-8.
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