Using long-read sequencing to detect imprinted DNA methylation

 


Scott Gigante 1,6*†, Quentin Gouil 2,3†, Alexis Lucattini 4, Andrew Keniry 2,3, Tamara Beck 2, Matthew Tinning 4, Lavinia Gordon 4, Chris Woodruff 1, Terence P. Speed 1,5ˆ, Marnie E. Blewitt 2,3ˆ and Matthew E. Ritchie 2,3,5ˆ

 

1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 Australia.
2 Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 Australia.
3 Department of Medical Biology, The University of Melbourne, Parkville, 3010 Australia.
4 Australian Genome Research Facility, 1G Royal Parade, Parkville, 3052 Australia.
5 School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010 Australia.
6 Department of Genetics, Yale University, New Haven, 06520 USA.
† Equal first author
ˆ Equal last author

bioRxiv preprint

The preprint of this study can be found under doi:10.1101/445924

Genome Browser

Explore the data for yourself on JBrowse.

Data

All sequencing data are deposited on ENA under study accession ERP109201.

RNA-seq sample clustering can be viewed on the Glimma MDS plot.

Parent-of-origin differential expression can be explored on the Glimma report, which includes an MD-plot, gene counts by replicate and a summary table.

Strain-biased expression can be explored on the Glimma report by strain, which includes an MD-plot, gene counts by replicate and a summary table.

Table of imprinted genes.

Table of DMRs.

Code

All code necessary to reproduce the analyses is available from Scott Gigante's Github folder.


Comments/Questions? Contact mritchie@wehi.edu.au.
Last modified: 5th September 2018