Yale TAR Track Settings
 
Yale RNA Transcriptionally Active Regions (TARs)   (All ENCODE Transcript Levels tracks)

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 Yale TAR Neutro  Yale Neutrophil RNA Transcriptionally Active Region (TAR)   Data format 
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 Yale TAR Plcnta  Yale Placenta RNA Transcriptionally Active Region   Data format 
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 Yale TAR NB4 RA  Yale NB4 RNA, TAR, Treated with Retinoic Acid   Data format 
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 Yale TAR NB4 TPA  Yale NB4 RNA, TAR, Treated with 12-O-tetradecanoylphorbol-13 Acetate (TPA)   Data format 
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 Yale TAR NB4 Un  Yale NB4 RNA, TAR, Untreated   Data format 
Source data version: ENCODE Oct 2005 Freeze
Assembly: Human May 2004 (NCBI35/hg17)

Description

This track shows the locations of transcriptionally active regions (TARs)/transcribed fragments (transfrags) 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).
  • poly(A)+ and Total RNA for HeLa S3 (3 biological replicates for each)

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:

Display Conventions and Configuration

TARs are represented by blocks in the graphical display. This composite annotation track consists of several subtracks that are listed at the top of the track description page. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide.

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

Methods

The data from biological & technical replicates were quantile-normalized to each other and then median scaled to 25. 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. Transcribed regions (TARs/transfrags) were then identified using a signal theshold determined from a 95% false positive rate (FPR) using the bacterial negatives on the array, as well as a maximum gap of 50 bp and a minimum run of 40 bp (between oligonucleotide positions). The TAR sites that are reported start and end at the middle nucleotide of the beginning and ending oligonucleotide probes.

Verification

Transcribed regions (TARs/transfrags), as determined by individual biological samples, were compared to ensure significant overlap.

Credits

These data were 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).