Description
This track is produced as part of the ENCODE Transcriptome Project.
Transcription of different
RNA extracts from different
sub-cellular localizations in different
cell lines
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 Transfrags data are lifted over from the hg18 assembly. The Raw Transfrags are available for download only. Other views are available on the hg18 assembly.
Display Conventions and Configuration
To show only selected subtracks, uncheck the boxes next to the tracks that
you wish to hide.
- Transfrags
- The filtered transfrags view excludes repeats and other known annotations
including:
tRNAs and rRNAs, mi/snoRNAs, things mapping to the mitochondrial or Y
chromosomes, and many predicted snoRNAs and miRNAs.
Methods
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
these
protocols.
Each RNA fraction was converted into double-stranded cDNA using
random hexamers,
labeled and hybridized to a tiling 91-array set containing probes against the
non-repetitive
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
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.
Verification
The reproducibility of the labeling method was assessed separately. Three
independent
technical replicates were generated from the same RNA pool for each RNA
preparation and
hybridized to duplicate arrays (two technical replicates) that contain the
ENCODE regions.
Labeled RNA samples were then pooled and hybridized to the tiling 91-array
set spanning
the whole genome. Transcribed regions (transfrags; see the Raw Transfrags
view) were
generated from the Raw Signal by merging genomic positions to which
probes
are mapped. This merging was based on a 5% false positive rate cutoff in
negative
bacterial controls, a maximum gap (MaxGap) of 40 base-pairs and minimum run
(MinRun)
of 40 base-pairs.
Release Notes
The track data were originally computed on the Human March 2006 assembly (hg18);
the coordinates of the Transfrags were transformed to this assembly using UCSC's liftOver
program.
Credits
These data were generated and analyzed by the transcriptome group at
Affymetrix
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.
Contact:
Tom Gingeras
References
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):1149-54.
Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR.
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.
Publications
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al.
Evidence for transcript networks composed of chimeric RNAs in human cells.
PLoS One. 2012;7(1):e28213.
Data Release Policy
Data users may freely use ENCODE data, but may not, without prior
consent, submit publications that use an unpublished ENCODE dataset until
nine months following the release of the dataset. This date is listed in
the Restricted Until column, above. The full data release policy
for ENCODE is available
here.
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