## Description

This track shows the locations of forward (+) and reverse (-) strand transcriptionally-active regions (TARs)/transcribed fragments (transfrags), for human NB4 cell total RNA and for human placenta Poly(A)+ RNA, hybridized to the Yale Maskless Array Synthesizer (MAS) ENCODE oligonucleotide microarray, transcription mapping design #1. This array has 36-mer oligonucleotide probes approximately every 36 bp (i.e. end-to-end) covering all the non-repetitive DNA sequence of the ENCODE regions ENm001 - ENm012. See NCBI GEO accession GPL2105 for details of this array design.

These TARs/transfrags are based on a transcript map combining hybridization intensities from three biological replicates, each with at least two technical replicates. Arrays were hybridized using either Nimblegen standard protocol, or the protocol described in Bertone et al. (2004). The label of each subtrack in this annotation indicates the specific protocol used for that particular data set.

## Methods

A score was assigned to each oligonucleotide probe position by combining two or more technical replicates and by using a sliding window approach. Within a sliding window of 160 bp (corresponding to 5 oligos), the hybridization intensities for all replicates of each oligonucleotide probe were compared to their respective array median intensity. Within the window and across all the replicates, the number of probes above and below their respective median was counted. Using the sign test, a one-sided P-value was then calculated and a score defined as score=-log(p-value) was assigned to the oligo in the center of the window.

Three independent biological replicates were generated, and each was hybridized to at least two different arrays (technical replicates). Transcribed regions (TARs/transfrags) were then identified using a score threshold of 95th percentile as well as a maximum gap of 80 bp and a minimum run of 50 bp (between oligonucleotide positions), effectively allowing a gap of one oligo and demanding the TAR/transfrag to encompass at least 3 oligos.

## 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 the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University.

## References

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.
Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M, The transcriptional activity of human Chromosome 22, Genes Dev, 2003 Feb 15;17(4):529-40.
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M, Global identification of human transcribed sequences with genome tiling arrays, Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR, Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution, Science. 2005 May 20;308(5725):1149-54. Epub 2005 Mar 24.