Open Access Research article

Unique small RNA signatures uncovered in the tammar wallaby genome

James Lindsay12, Dawn M Carone13, Judy Brown14, Laura Hall1, Sohaib Qureshi1, Sarah E Mitchell1, Nicholas Jannetty1, Greg Hannon5, Marilyn Renfree67, Andrew Pask1, Michael O’Neill1 and Rachel O’Neill1*

Author Affiliations

1 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA

2 Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA

3 Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA

4 Department of Allied Health Sciences, University of Connecticut, Storrs, CT, 06269, USA

5 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA

6 Australian Research Council Centre of Excellence in Kangaroo Genomics, Victoria, Australia

7 Department of Zoology, The University of Melbourne, Victoria, 3010, Australia

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BMC Genomics 2012, 13:559  doi:10.1186/1471-2164-13-559

Published: 17 October 2012

Additional files

Additional file 1: Table S1:

Ensembl-predicted miRNA genes confirmed by our pipeline. Those with transcripts identified in tammar embryo transcriptomes are indicated, as are the miRNA genes confirmed by miRDeep2 and the miRBase orthologs.

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Additional file 2: Table S2:

Complete annotations for all piRNAs in tammar testis. Annotation names based on RepBase entries.

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Additional file 3: Table S3:

Complete annotations for all crasiRNAs in tammar fibroblast cells (A) and testis (B). Annotation names based on RepBase entries.

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Additional file 4: Figure S1:

Primed in situ hybridization for localization of crasiRNA progenitor sequences, (green/red) to tammar metaphase chromosomes (grey). A. L1-2. B. L1-3. C. LTRX. D. LTR4. E. RTE2.

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Additional file 5: Figure S2:

Screen capture from Broad institute Integrative Genomics Viewer (IGV) showing a tammar contig with mapping anti-CENP-A ChIP seq reads, crasiRNA reads and repeats as annotated by Repeat Modeler. Top of each panel are the coverage profiles and bottom (not shown in full detail) are alignment locations of individual reads.

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Additional file 6: Figure S3:

A. Pipeline of the small RNA processing for miRNAs. The “small RNA reads” and “gene annotation” trapezoids represent the input to the miRNA pipeline. The “preprocess”, “map”, “hairpin identification” and “miRNA identification” blue boxes are the stages in the pipeline which filter out the true miRNA reads from the noise. Finally the miRNA genes and targets are identified from the hairpins, miRNA and gene annotations. Each of these steps is explained in detail in the methods section. B. Northern validation of (left) miRNA gene (miRNA20A) and (right) crasiRNA (SINE28).

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Additional file 7: Table S4:

Primers used in PRINS.

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