miRNA

The Broad Institute and The Genome Analysis Centre have produced an annotated miRNA track for the dog genome assembly.

These tracks represent the precursor (hairpin) structures of both known and novel miRNAs for the dog, as detailed below, as well as expression in the various tissues surveyed.

Display Conventions and Configuration

Known miRNAs have their associated mirBase IDs associated with them, where novel ones simply have their genomic locations and no annotation beyond that. The miRNA have been classified as either high or low confidence (with scores of 1000 or 0, respectively,) as detailed below.

Expression levels are displayed via a wiggle plot, with levels between 0 and 1 as outlined below.

Methods

Annotations were derived from RNAseq data generated by the Broad Institute and analyzed at The Genome Analysis Centre. The annotation process was as follows:

1. Reads were mapped to the CanFam3.1 genome assembly.
2. Novel miRNAs were predicted using both miRCat and miRDeep2.
3. The predicted smallRNA secondary structures and read alignments were tested for consistency against Drosha/Dicer processing.
4. Using the existing miRBase canine annotation3, smallRNA reads were aligned to hairpins. If they had good expression evidence, secondary structure and read alignments were called at "high" confidence (score = 1000), others were called "low" confidence (score = 0).
5. After generating a list of putative homologues of canine miRNAs (BLASTing all animal miRBase miRNAs against the dog genome, accepting as putative homologues those with an e-value <= 10-6,) the mature miRBase miRNAs were mapped to these putative precursors. Any with 1 or 0 mismatches were accepted at potential miRNAs. These miRBase homologues were also called at either "high" or "low" coverage.

Credits

RNA-Seq data was generated at the Broad Institute by Ross Swofford and the Genomics Platform. The miRNA annotation was generated by Drs. Simon Moxon and Luca Penso-Dolfin at The Genome Analysis Centre. Dr. Kerstin Lindblad-Toh of the Broad Institute, Uppsala University and SciLifeLab and Dr. Federica di Palma of The Genome Analysis Centre provided scientific leadership & support for the project.

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