enrightlab / bitetti_et_al_codebase

Supporting code for:"A conserved RNA regulates miRNA turnover and animal behavior through a near-perfect miRNA site"

Supporting code for:

A conserved RNA regulates miRNA turnover and animal behavior through a near-perfect miRNA site

Angelo Bitetti^1,2,3,*, Allison C Mallory^1,2,3,*, Claudia Carrieri⁴, Elisabetta Golini⁵, Hector Carreño Gutierrez⁶, Emerald Perlas⁷, Yuvia A. Pérez-Rico^1,2,3,8, Glauco P. Tocchini-Valentini⁵, Anton J. Enright⁹, William H. J. Norton⁶, Silvia Mandillo⁵, Dónal O'Carroll⁴ and Alena Shkumatava^1,2,3

*These authors contributed equally to this work.

<sub>1. Institut Curie, 26 Rue d’Ulm, 75248 Paris Cedex 05, France.
2. CNRS UMR3215, 75248 Paris Cedex 05, France.
3. INSERM U934, 75248 Paris Cedex 05, France..
4. MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, UK.
5. Consiglio Nazionale delle Ricerche, Istituto di Biologia Cellulare e Neurobiologia, European Mouse Mutant Archive-Infrafrontier-International Mouse Phenotyping Consortium, I-00015 Monterotondo Scalo (Rome), Italy.
6. Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK.
7. European Molecular Biology Laboratory (EMBL), Mouse Biology Unit, Monterotondo Scalo, Italy.
8. INSERM, U900, 75248 Paris Cedex 05, France.
9. European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.</sub>

Code used for small RNA analyses

The codebase describes the small RNA analysis and was authored by Anton Enright ([email protected]) March-May 2017.

• The R/BioConductor code and results (markdown) for small RNA analysis
• The Rmarkdown for small RNA analysis
• The final table (tab-delimited) of normalised miRNA counts and statistical results for each miR

Initial Data

• The raw count-table derived from the chimiRa mapping tool
• The experimental design (pdata) file
• An accessory table containing small RNA lengths extracted from the chimiRa mapping tool

Version Information

ChimiRa was used to trim adapters and map reads to microRNA precursors
R version used was: R 3.3.1 (2016-06-21) -- "Bug in Your Hair"
BioConductor version used was: Bioconductor version 3.4

Dependencies: RColorBrewer, gplots, DESeq2, reshape2, ggplot2