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ENCODE Long RNA-seq and Short RNA-seq Contigs and Signal

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Assembly: Human Feb. 2009 (GRCh37/hg19)

Note: ENCODE Project

Description

This set of data tracks represents the set of RNA elements (contigs) and signals based on Long and Short RNA-seq datasets. The data tracks were generated by the ENCODE Analysis Working Group (AWG) based on a uniform processing pipeline. The datasets are based on the January 2011 internal data freeze. These datasets were used in all downstream analysis pipelines by members of the ENCODE Consortium and are one of the primary sources of data referenced in the ENCODE Integrative analysis paper (ENCODE Project Consortium, 2012).

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.

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.

Elements

Contigs are continuous regions covered by uniquely alligned reads from shotgun long RNA-seq. Gaps in coverage of up to 25 bases are allowed. Contigs are strand-specific, but contigs with more than 9 times more antisense than sense signal are filtered as possible artifacts of strand-specific library construction. Contigs are called on merged biological replicates, but scored against individual replicates to evaluate reproducibility using the irreproducible detection rate (IDR) framework. Calls were filtered at a local IDR cutoff of 0.1. The bedscore (column 5) for long RNA contigs is computed as min(1000,100*log(summed_bpkm*100+1)), where BPKM is "Bases Per Kilobase per Million mapped bases", averaged between the replicates.

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 > 0.90 between biological replicates. Additional data can be found at the Transcriptome Data Portal.

References

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74.

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 Sep;21(9):1543-51.

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 on the track configuration page and the download page. The full data release policy for ENCODE is available here.

There is no restriction on the use of these specific tracks.

Contact

Thomas Gingeras