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RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL   (All Expression tracks)

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  RNA Extract: Long PolyA- Long PolyA+ Total RNA
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 GM12878  Whole Cell  Total RNA  GM12878 whole cell total Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-12-10 
 
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 GM12878  Cytosol  Long PolyA-  GM12878 cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-09-09 
 
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 GM12878  Cytosol  Long PolyA+  GM12878 cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-21 
 
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 GM12878  Nucleus  Long PolyA-  GM12878 nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-21 
 
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 GM12878  Nucleus  Long PolyA+  GM12878 nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-01-01 
 
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 GM12878  Nucleolus  Total RNA  GM12878 nucleolus total Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-05-27 
 
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 K562  Whole Cell  Total RNA  K562 whole cell total Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-25 
 
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 K562  Cytosol  Long PolyA-  K562 cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-22 
 
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 K562  Cytosol  Long PolyA+  K562 cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-22 
 
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 K562  Polysome  Long PolyA-  K562 polysome polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-21 
 
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 K562  Nucleus  Long PolyA-  K562 nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-22 
 
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 K562  Nucleus  Long PolyA+  K562 nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-22 
 
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 K562  Nucleoplasm  Total RNA  K562 nucleoplasm total Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-12-10 
 
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 K562  Chromatin  Total RNA  K562 chromatin total Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-10-09 
 
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 K562  Nucleolus  Total RNA  K562 nucleolus total Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-11-04 
 
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 HepG2  Cytosol  Long PolyA-  HepG2 cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-02-27 
 
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 HepG2  Cytosol  Long PolyA+  HepG2 cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-02-27 
 
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 HepG2  Nucleus  Long PolyA-  HepG2 nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-04-17 
 
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 HepG2  Nucleus  Long PolyA+  HepG2 nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-04-17 
 
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 HepG2  Nucleolus  Total RNA  HepG2 nucleolus total Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-05-27 
 
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 NHEK  Cytosol  Long PolyA-  NHEK cytosol polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-02-27 
 
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 NHEK  Cytosol  Long PolyA+  NHEK cytosol polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-02-27 
 
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 NHEK  Nucleus  Long PolyA-  NHEK nucleus polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-03-12 
 
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 NHEK  Nucleus  Long PolyA+  NHEK nucleus polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2010-03-12 
 
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 prostate  Whole Cell  Long PolyA-  Prostate whole cell polyA- Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-24 
 
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 prostate  Whole Cell  Long PolyA+  Prostate whole cell polyA+ Microarray Transfrags from ENCODE Affy/CSHL    Schema   2009-08-24 
     Restriction Policy
Downloads
Data coordinates converted via liftOver from: Mar. 2006 (NCBI36/hg18)

Description

This track is produced as part of the ENCODE Transcriptome Project. Transcription of different RNA extracts from different sub-cellular localizations in different cell lines is compared in companion experiments using three different technologies: tiling arrays, RNA-seq using Solexa, and RNA-seq using SOLiD. The tiling array data are shown in this track. The Transfrags data are lifted over from the hg18 assembly. The Raw Transfrags are available for download only. Other views are available on the hg18 assembly.

Display Conventions and Configuration

To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide.

Transfrags
The filtered transfrags view excludes repeats and other known annotations including: tRNAs and rRNAs, mi/snoRNAs, things mapping to the mitochondrial or Y chromosomes, and many predicted snoRNAs and miRNAs.

Methods

Cells were grown according to the approved ENCODE cell culture protocols. RNA molecules longer than 200 nt and present in RNA population isolated from different subcellular compartments (such as cytosol, nucleus, polysomes and others) were fractionated into polyA+ and polyA- fractions as described in these protocols. Each RNA fraction was converted into double-stranded cDNA using random hexamers, labeled and hybridized to a tiling 91-array set containing probes against the non-repetitive portion of the human genome tiled on average every 5 bp (center-to-center of each consecutive 25-mers).

All arrays were scaled to a median array intensity of 330. Within a sliding 61 bp window centered on each probe, an estimate of RNA abundance was found by calculating the median of all pairwise average PM-MM values, where PM is a perfect match and MM is a mismatch. Kapranov et al. (2002), Cheng et al. (2005) , Kapranov et al. (2007), and Cawley et al. (2004) are good references for the experimental methods. Cawley et al. also describes the analytical methods.

Verification

The reproducibility of the labeling method was assessed separately. Three independent technical replicates were generated from the same RNA pool for each RNA preparation and hybridized to duplicate arrays (two technical replicates) that contain the ENCODE regions. Labeled RNA samples were then pooled and hybridized to the tiling 91-array set spanning the whole genome. Transcribed regions (transfrags; see the Raw Transfrags view) were generated from the Raw Signal 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 40 base-pairs and minimum run (MinRun) of 40 base-pairs.

Release Notes

The track data were originally computed on the Human March 2006 assembly (hg18); the coordinates of the Transfrags were transformed to this assembly using UCSC's liftOver program.

Credits

These data were generated and analyzed by the transcriptome group at Affymetrix and Cold Spring Harbor Laboratories: P. Kapranov, I. Bell, E. Dumais, J. Drenkow, J. Dumais, N. Garg, M. Lubinsky, Carrie A. Davis, Huaien Wang, Kimberly Bell, Jorg Drenkow, Chris Zaleski, and Thomas R. Gingeras.

Contact: Tom Gingeras

References

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.

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.

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.

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007 Jun 8;316(5830):1484-8.

Publications

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.