## 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).