Yale RNA Tracks
 
Yale RNA (Neutrophil, Placenta and NB4 cells) tracks   (All Pilot ENCODE Transcription tracks)

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Yale MAS RNA  Yale Maskless Array Synthesizer, RNA Transcript Map  Source data version: ENCODE June 2005 Freeze
Yale MAS TAR  Yale Maskless Array Synthesizer, RNA Transcriptionally Active Regions  Source data version: ENCODE June 2005 Freeze
Yale RNA  Yale RNA Transcript Map (Neutrophil, Placenta and NB4 cells)  Source data version: ENCODE Oct 2005 Freeze
Yale TAR  Yale RNA Transcriptionally Active Regions (TARs)  Source data version: ENCODE Oct 2005 Freeze

Overview

This super-track combines related tracks from Yale Transcript Map analysis. These tracks contain transcriptome data from different cell lines and biological samples as well as analysis of transcriptionally active regions (TARs).

Experiments were performed with Yale MAS (Maskless Array Synthesizer) ENCODE oligonucleotide microarray (see NCBI GEO GPL2105 for details of this array design) as well as the Affymetrix ENCODE oligonucleotide microarray. Multiple biological samples were assayed, such as total RNA from human NB4 cells. Experiments also included chemical treatments such as retinoic acid (RA) treatments.

Credits

Yale MAS RNA, Yale MAS TAR

These data were generated and analyzed by the the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University.

Yale RNA, Yale TAR

These data were generated and analyzed by the Yale/Affymetrix collaboration among the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University and Tom Gingeras at Affymetrix.

Yale RACE

These data were generated and analyzed by the lab of Mark Gerstein at Yale University.

References

Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M et al. Global identification of human transcribed sequences with genome tiling arrays. Science. 2004 Dec 24;306(5705):2242-6.

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

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.

Kluger Y, Tuck DP, Chang JT, Nakayama Y, Poddar R, Kohya N, Lian Z, Ben Nasr A, Halaban HR et al. Lineage specificity of gene expression patterns. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6508-13.

Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P et al. The transcriptional activity of human Chromosome 22. Genes Dev. 2003 Feb 15;17(4):529-40.