Cufflinks Transcripts from RNA-Seq from LUPA Consortium Samples

This track contains all of the raw Cufflinks assembled transcripts for each RNA-Seq library generated by the Broad Institute using RNA-Seq data derived from samples from several member labs of the LUPA Consortium. These data will be used in a FUTURE annotation process,and were NOT part of the annotation process described in Hoeppner et. al.

This design provides a source of new tissues that will be of high interest to catalog more specifically long non-coding RNAs (lncRNAs) that are highly tissue specific and are known to play a major roles in genetic diseases and cancer.

Display Conventions and Configuration

Tracks are tissue specific. Poly-A selected libraries were generated accross 13 tissue types

Methods

The sequences were aligned via TopHat and transcripts were assembled assembled via the Cufflinks RNA-Seq assembly software. See Hoeppner et. al. 1 for more detailed methods for TopHat and Cufflinks assembly processes. .

Credits

Sample collection was coordinated by Drs. Veronique Duranthon & Christophe Hitte of the University of Rennes, France. RNA-Seq data was generated at the Broad Institute. Cufflinks assemblies were generated by Jason Turner-Maier at the Broad Institute. Dr. Kerstin Lindblad-Toh of the Broad Institute and the SciLifeLab of Uppsala University provided scientific management 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 g roup: vertebrategenomes@broadinstitute.org