Description

This track shows an estimate of RNA abundance (transcription) over the first 24 hours of D. melanogaster development in two hour increments, measured by a tiling array as described in Manak et al. (2006) (see References). Composite signals are shown in separate subtracks for each of the twelve timepoints.

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 timepoints.

Methods

The data were processed into signal and transfrags as described in Cheng et al. (2005) and Kampa et al. (2004). The data from replicate arrays were quantile-normalized and all arrays were scaled to a median array intensity of 25. 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. This data set was originally created for dm2(BDGP R4) and then lifted over to dm3(BDGP R5).

Verification

Samples were hybridized to duplicate arrays (three 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 90 base-pairs (see the Affy TransFrags track for the merged regions).

Credits

These data were generated and analyzed by the Tom Gingeras group at Affymetrix.

References

Please see the Affymetrix Transcriptome site for a project overview and additional references to Affymetrix tiling array publications.

Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005 May 20;308(5725):1149-54. PMID: 15790807

Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 2004 Mar;14(3):331-42. PMID: 14993201; PMC: PMC353210

Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, Long J, Cheng J, Bell I, Ghosh S, Piccolboni A et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet. 2006 Oct;38(10):1151-8. PMID: 16951679