Affy RNA Signal Track Settings
 
Affymetrix PolyA+ RNA Signal   (All ENCODE Transcript Levels tracks)

Display mode:       Reset to defaults

Type of graph:
Track height: pixels (range: 16 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: -1168 to 1591.5)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
List subtracks: only selected/visible    all    ()  
hide
 Configure
 Affy RNA GM06990  Affymetrix PolyA+ RNA (GM06990) Signal   Data format 
hide
 Configure
 Affy RNA HeLa  Affymetrix PolyA+ RNA (HeLa) Signal   Data format 
hide
 Configure
 Affy RNA RA 0h  Affymetrix PolyA+ RNA (retinoic acid-treated HL-60, 0hrs) Signal   Data format 
hide
 Configure
 Affy RNA RA 2h  Affymetrix PolyA+ RNA (retinoic acid-treated HL-60, 2hrs) Signal   Data format 
hide
 Configure
 Affy RNA RA 8h  Affymetrix PolyA+ RNA (retinoic acid-treated HL-60, 8hrs) Signal   Data format 
hide
 Configure
 Affy RNA RA 32h  Affymetrix PolyA+ RNA (retinoic acid-treated HL-60, 32hrs) Signal   Data format 
    
Source data version: ENCODE Oct 2005 Freeze
Assembly: Human May 2004 (NCBI35/hg17)

Description

This track shows an estimate of RNA abundance (transcription) for all ENCODE regions for several cell types. Retinoic acid-stimulated HL-60 cells were harvested after 0, 2, 8, and 32 hours. Purified cytosolic polyA+ RNA from unstimulated GM06990 and HeLa cells, as well as purified polyA+ RNA from the RA-stimulated HL-60 samples, was hybridized to Affymetrix ENCODE oligonucleotide tiling arrays, which have 25-mer probes tiled every 22 bp on average in the non-repetitive ENCODE regions. Composite signals are shown in separate subtracks for each cell type and for each of the four timepoints for RA-stimulated HL-60.

Data for all biological replicates can be downloaded from Affymetrix in wiggle, cel, and soft 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.

Color differences among the subtracks are arbitrary. They provide a visual cue for distinguishing between the different cell types and timepoints.

Methods

The data from replicate arrays were quantile-normalized (Bolstad et al., 2003) and all arrays were scaled to a median array intensity of 22. Within a sliding 101 bp window centered on each probe, an estimate of RNA abundance (signal) was found 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; Cawley et al. also describes the analytical methods.

Verification

Three independent 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 50 base-pairs and minimum run (MinRun) of 40 base-pairs (see the Affy TransFrags track for the merged regions). A random subset of transfrags were verified by RACE where the RACE primers were designed based on the sequences of the transfrags.

Credits

These data were generated and analyzed by the Gingeras/Struhl collaboration with the Tom Gingeras group at Affymetrix and the Kevin Struhl group at Harvard Medical School.

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).