## Description

This track displays transcriptome data from tiling GeneChips produced by Affymetrix. For the complete non-repetitive portion of the human genome, more than 256 million probe pairs were tiled every 5 bp in non-repeat-masked areas and hybridized to whole-cell short RNA (<200 nucleotides) from two different cell lines. Note that the female cell lines HeLa, SK-N-AS, and U87MG do not contain data for chrY. Data were collected using a strand-specific methodology that allows separate measurements for top strand (sense) and bottom strand (antisense) RNA signals. For experimental details and results, see Kapranov et al. in the References section below.

This track shows the coordinates of transcribed fragments (transfrags) representing short RNAs. A separate track -- "Affy Tx sRNA signals" -- contains signals (PM-MM values) for each probe pair plotted against its genomic coordinates (see Kapranov et al. in the References section below).

## Display Conventions and Configuration

This annotation follows the display conventions for composite tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. For more information about the graphical configuration options, click the Graph configuration help link. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide.

## Methods

Genomic regions corresponding to the sRNA transcripts were mapped for the plus or the minus strands of the genome and for HepG2 and HeLa cell lines respectively. The following analysis steps were performed:

1. Replicate arrays were quantile-normalized and the median intensity (using both PM and MM intensities) of each array was scaled to a target value of 20.
2. The expression level was estimated for each mapped probe position without application of a smoothing window. These data are displayed in the track "Affy Tx sRNA Sig". This was followed by generation of transfrags as follows:
   - probes with intensities corresponding to the 98th percentile of all the PM-MM probe intensities were identified.
   - transfrags were determined by connecting adjacent positive probes with a maximum allowable gap of four nucleotides and a minimum run of seven nucleotides (at least two consecutive positive probes with no negative probes between), and must be called positive reproducibly in both biological replicas.
   - to further prioritize the transfrag maps, the intensities of all transfrags were calculated based on the composite signals of the two biological replicas, and transfrags corresponding to the top 25 quartile were used for further analysis.
3. In addition, several successive steps were performed to avoid potentially cross-hybridizing sequences and/or those that mapped to potentially non-unique regions. Transfrags were discarded if they overlapped pseudogenes or harbored low-complexity or repetitive sequences. The resulting maps are believed to represent a very conservative view of the sRNA population in the cell.

## Credits

Data generation and analysis were performed by the transcriptome group at Affymetrix with assistance from colleagues at the University of Leipzig, Fraunhofer Institute, and University of Vienna: P. Kapranov, J. Cheng, S. Dike, D.A. Nix, R. Duttagupta, A.T. Willingham, P.F. Stadler, J. Hertel, J. Hackermüller, I.L. Hofacker, I. Bell, E. Cheung, J. Drenkow, E. Dumais, S. Patel, G. Helt, M. Ganesh, S. Ghosh, A. Piccolboni, V. Sementchenko, H. Tammana, T.R. Gingeras.

Questions or comments about this annotation? Email genome@soe.ucsc.edu.

## References

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.