Long non-coding RNAs

The Broad Institute and Uppsala University have jointly produced an improved canine annotation by using RNA-Seq from ten canine tissues and a novel lift-over process for human annotations. A manuscript describing this has been submitted.

This track contains all transcripts that are considered long-non coding RNAs (lncRNAs.)

Display Conventions and Configuration

Every transcript isoform has both a unique ID and a more detailed annotation status (according to the schema laid out in Hoeppner et. al., see References.)

In addition, every transcript has an accompanying expression value based on the underlying RNA-Seq data used to generate the transcripts. Expression is measured in FPKM (fragments per kilobase of exon per million fragments mapped.) Expression data is listed for each library type generated. Two types of libraries (polyA selected and DSN normalized) and a panel of tissues were used for this annotation

Methods

Annotations were derived from RNAseq data generated by the Broad Institute, as well as the Ensembl dog and human annotations. The RNAseq reads were assembled using the Cufflinks pipeline and then merged with the Ensembl dog and human-based annotations. See Hoeppner et al. for more detailed methods.

Credits

RNA-Seq data was generated at the Broad Institute by Ross Swofford and the Genomics Platform. The annotation pipeline was developed by Drs. Manfred Grabherr & Marc Hoeppner at Uppsala University along with Jason Turner-Maier and Jeremy Johnson at the Broad Institute Dr. Kerstin Lindblad-Toh of the Broad Institute, Uppsala University and SciLifeLab provided scientific leadership for the project.

References

Hoeppner et. al., An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS ONE 9(3): e91172. doi: 10.1371/journal.pone.0091172.

Contact

For questions or more information on the data in this Track Hub, please contact the Broad Institute Vertebrate Genome Biology group: vertebrategenomes@broadinstitute.org