## Description

These tracks were generated by the ENCODE Consortium. They contain information about human RNAs > 200 nucleotides in length that were obtained as short reads from the Illumina GAIIx platform. Data are available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, there are also data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, see the RIKEN CAGE Loc track), Small RNA-seq (<200 nucleotides, see the CSHL Sm RNA-seq track) and Pair-End di-TAG-RNA (PET-RNA, see the GIS RNA PET track) datasets available from the same biological replicates.

## Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here.

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

Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments.

Contigs
  The Contigs represent blocks of overlapping mapped reads from the pooled biological replicates.
Raw Signals
  The Plus Raw Signal and Minus Raw Signal views show the density of mapped reads on the plus and minus strands (wiggle format), respectively.
Alignments
  The Alignments view shows individual reads mapped from pooled biological replicates to the genome and indicates where bases may mismatch. Every mapped read is displayed, i.e. uncollapsed. The alignment file follows the standard SAM format of Bowtie output. See the Bowtie Manual for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format.
Splice Junctions
  Subset of aligned reads that cross splice junctions.

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Additional views are available on the Downloads page.

## Methods

### Cell Culture

Cells were grown according to the approved ENCODE cell culture protocols.

### Library Preparation

The published cDNA sequencing protocol was used. This protocol generates directional libraries and reports the transcripts' strand of origin. Exogenous RNA spike-ins (Round 5, pool 14), in development at National Institutes Standards Technology, were added to each endogenous RNA isolate and carried through library construction and sequencing. The Illumina PhiX control library was also spiked-in at 1% to each completed human library just prior to cluster formation. Accompanying each RNA-seq dataset is a “Protocol Document,” available for download. This document contains details about the RNA isolations and treatments, library construction, spike-ins as well as quality control figures for individual libraries. The spike-in sequence and the concentrations are available for download in the supplemental directory.

### Sequencing and Mapping

The libraries were sequenced on the Illumina GAIIx platform to an average depth of ~200 million reads (100 million mate-pairs). The data were mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information about STAR, including the parameters used for these data, is available from the Gingeras lab.

The following processed “elements” data files are available for download. These elements were assessed for reproducibility using a nonparametric irreproducible detection (IDR) rate script. The IDR values for each element are included in the files for end-users to use as a threshold. An IDR value of 0.1 means that the probability of detecting that element in a third experiment equivalent in depth to the sum of the bioreplicates is 90%. In addition, expression values for annotated genes, transcripts and exons were computed. Further explanation of these files is available for download in the supplemental directory.

## Verification

FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated for annotated Gencode exons and Spearman values were compared. In general, Rho values are > .90 between biological replicates. Additional quality control metrics for the samples can be found Transcriptome Data Portal.

## Release Notes

This is release 2 (Nov 2011) of this track for hg19. This is Release 1 (Oct 2011) of this track for hg19. It includes data from the hg18 releases that has been remapped to hg19 (GM12878 and K562 Total RNA whole cell and K562 PolyA+ RNA cytosol) as well as novel data from 13 additional cell lines and 4 additional cell localizations, as well as some PolyA- samples. The signals are now in bigWig format. The alignments are in BAM format. The newer data all have Bio Replicate numbers and Protocol ID numbers that can be used to link the samples with other experiments. Every experiment has extensive analysis and a protocol document available for download only.

## Credits

These data were generated and analyzed by the transcriptome group at Cold Spring Harbor Laboratories and the Center for Genomic Regulation (CRG in Barcelona), who are participants in the ENCODE Transcriptome Group.

Contacts: Carrie Davis (experimental), Alex Dobin (computational), Felix Schlesinger (computational), Tom Gingeras (primary investigator), and Roderic Guigo’s group at the CRG.

## References

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011 Aug 4.

Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct; 37(18):e123.

## 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.