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).
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).
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