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
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.
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.
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,
Large-scale transcriptional activity in chromosomes 21 and 22.
Science. 2002 May 3;296(5569):916-9.