Overview

This super-track combines related tracks of transcriptome data generated by the Affymetrix/Harvard ENCODE collaboration. These tracks show an estimate of RNA abundance (transcription) and the locations of sites showing transcription for all ENCODE regions for various cell types, including HL-60 (leukemia), GM06990 (lymphoblastoid), and HeLa (cervical carcinoma).

RNA was isolated at multiple time points after drug treatment, and hybridized to Affymetrix ENCODE oligonucleotide tiling arrays. Data are displayed as signals (transcript abundance) and transfrags (sites of transcription).

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

Credits

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

References

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

Bolstad BM, Irizarry RA, Astrand M, and Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 Jan 22;19(2):185-93.

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004 Feb 20;116(4):499-509.

Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002 May 3;296(5569):916-9.