## Description

This track shows the transcript map of signal intensity (estimating RNA abundance) for the following, hybridized to the Affymetrix ENCODE oligonucleotide microarray:

- human neutrophil (PMN) total RNA (10 biological samples from different individuals)
- human placental Poly(A)+ RNA (3 biological replicates)
- total RNA from human NB4 cells (4 biological replicates), each sample divided into three parts and treated as follows: untreated, treated with retinoic acid (RA), and treated with 12-O-tetradecanoylphorbol-13 acetate (TPA) (three out of the four original samples). Total RNA was extracted from each treated sample and applied to arrays in duplicate (2 technical replicates).

The human NB4 cell can be made to differentiate towards either monocytes (by treatment with TPA) or neutrophils (by treatment with RA). See Kluger et al., 2004 in the References section for more details about the differentiation of hematopoietic cells.

This array has 25-mer oligonucleotide probes tiled approximately every 22 bp, covering all the non-repetitive DNA sequence of the ENCODE regions. The transcript map is a combined signal for both strands of DNA. This is derived from the number of different biological samples indicated above, each with at least two technical replicates.

See the following NCBI GEO accessions for details of experimental protocols:

- GSE2678
- GSE2671
- GSE2679

## Display Conventions and Configuration

This annotation follows the display conventions for composite "wiggle" 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. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

Color differences among the subtracks are arbitrary. They provide a visual cue for distinguishing between the different data samples.

## Methods

The data from technical replicates were median-scaled and quantile-normalized to each other. Using a 101 bp sliding window centered on each oligonucleotide probe, a signal map (estimating RNA abundance) was generated by computing the pseudomedian signal of all PM-MM pairs (median of pairwise PM-MM averages) within the window, including replicates. Biological replicate signal maps were combined by quantile-normalizing them between replicates and computing the median signal at each oligonucleotide probe location.

## Verification

Independent biological replicates (as indicated above) were generated, and each was hybridized to at least two different arrays (technical replicates). Transcribed regions were then identified using a signal theshold of 90 percentile of signal intensities, as well as a maximum gap of 50 bp and a minimum run of 50 bp (between oligonucleotide positions). Transcribed regions, as determined by individual biological samples, were compared to ensure significant overlap.

## Credits

This data was generated and analyzed by the Yale/Affymetrix collaboration between the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University and Tom Gingeras at Affymetrix.

## References

Bertone, P., Stolc, V., Royce, T.E., Rozowsky, J.S., Urban, A.E., Zhu, X., Rinn, J.L., Tongprasit, W., Samanta, M. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306(5705), 2242-6 (2004).

Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308(5725), 1149-54 (2005).

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), 916-9 (2002).

Kluger, Y., Tuck, D.P., Chang, J.T., Nakayama, Y., Poddar, R., Kohya, N., Lian, Z., Ben Nasr, A., Halaban, H.R. et al. Lineage specificity of gene expression patterns. Proc Natl Acad Sci U S A 101(17), 6508-13 (2004).

Rinn, J.L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N.M., Hartman, S., Harrison, P.M., Nelson, F.K., Miller, P. et al. The transcriptional activity of human Chromosome 22. Genes Dev 17(4), 529-40 (2003).