Description
This track shows an estimate of RNA abundance (transcription) for chromosomes 21
and 22 for 5 cell lines and 11 tissues. The 5 cell lines used were: GM06990,
HepG2, K562, HeLaS3 and Tert-BJ; the 11 tissues used were: cerebellum, brain
frontal lobe, hippocampus, hypothalamus, fetal spleen, fetal kidney, fetal thymus,
ovary, placenta, prostate and testis. Purified cytosolic polyA+ RNA from GM06990,
HepG2 and Tert-BJ cell lines, as well as purified polyA+ RNA from whole cell
extracts of the remaining cell lines and tissues, were hybridized to Affymetrix
Chromosome 21_22_v2 oligonucleotide tiling arrays, which have 25-mer probes
spaced on average every 17 bp (center-center of each 25mer) in the non-repetitive
regions of human chromosomes 21 and 22. Composite signals are shown in separate
subtracks for each cell and tissue types.
Data for all biological replicates can be
downloaded from Affymetrix in wig, BED, and cel formats.
Display Conventions and Configuration
The subtracks within this composite annotation track may be configured
in a variety of ways to highlight different aspects of the displayed
data. The graphical configuration options for the subtracks are shown
at the top of the track description page, followed by a list of
subtracks. To show only selected subtracks, uncheck the boxes next to
the tracks that you wish to hide. For more information about the
graphical configuration options, click the Graph configuration help
link.
Methods
The data from replicate arrays were quantile-normalized (Bolstad et al.,
2003) and all arrays were scaled to a median array intensity of 330. Using two
different approaches: i) no sliding window ii) sliding 51-bp window centered on
each probe, an estimate of RNA abundance (signal) was computed by calculating
the median of all pairwise average PM-MM values, where PM is a perfect match
and MM is a mismatch. Both Kapranov et al. (2002) and Cawley
et al. (2004) are good references for the experimental methods. The
latter also describes the analytical methods.
Verification
Single biological replicates were generated and hybridized to duplicate arrays
(two technical replicates). Transcribed regions were generated from the
composite signal track 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 25 basepairs and minimum run (MinRun) of
25 basepairs (see the Affy TransFrags track for the merged regions).
Credits
These data were generated and analyzed by the collaboration of the following
groups: the Tom Gingeras group at Affymetrix, Roderic Guigo group at Centre
de Regulacio Genomica, Alexandre Reymond group at the University of Lausanne
and Stylianos Antonarakis group at University of Geneva.
References
Please see the Affymetrix
Transcriptome site for a project overview and additional references to
Affymetrix tiling array publications.
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. A
comparison of normalization methods for high density oligonucleotide
array data based on variance and bias. Bioinformatics 19(2),
185-193 (2003).
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A.,
Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams,
A. J., et al. Unbiased mapping of transcription factor binding sites along human
chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell
116(4), 499-509 (2004).
Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg,
R. L., Fodor, S. P., and Gingeras, T. R. Large-scale transcriptional activity in chromosomes 21 and
22. Science 296(5569), 916-919 (2002).