Resources
Software
IRFinder
A program for detecting intron retention from RNA-Seq experiments
https://github.com/williamritchie/IRFinder/wiki
IRFinder: assessing the impact of intron retention on mammalian gene expression. Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ, Bomane A, Cosson B, Eyras E, Rasko JE, Ritchie W. Genome Biol. 2017
miREval 2.0
A tool used discover miRNAs from genome sequences
http://mimirna.centenary.org.au/mireval/
miREval 2.0: a web tool for simple microRNA prediction in genome sequences. Gao D, Middleton R, Rasko JE, Ritchie W. Bioinformatics, 2013
mimiRNA
An online resource to provide reliable miRNA expression profiles
http://mimirna.centenary.org.au/mep/formulaire.html
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Ritchie W, Flamant S, Rasko JE. Bioinformatics, 2009
IRBase
The Intron Retention Database
Data Resources
Macrophage development and activation involve coordinated intron retention in key inflammatory regulators
mRNA sequencing and WGBS data: GSE130011MS data: PXD017391
Ctcf haploinsufficiency mediates intron retention in a tissue-specific manner
mRNA sequencing data: GSE140532
DNA methylation/hydroxymethylation regulate gene expression and alternative splicing during terminal granulopoiesis
Whole genome bisulfite sequencing of mouse promyelocytes and granulocytes: GSE85517
mRNA sequencing of mouse promyelocytes and granulocytes: GSE48307
reduced representation 5-hydroxymethylation profiling of mouse promyelocytes and granulocytes: PRJNA495696
Intron retention enhances gene regulatory complexity in vertebrates
RNA-seq data: SRP092128
Identification of nuclear-enriched miRNAs during mouse granulopoiesis
Microarray gene expression data: GSE57624
RBM3 regulates temperature sensitive miR-142–5p and miR-143 (thermomiRs), which target immune genes and control fever
Microarray gene expression data: GSE69343
Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation
mRNA sequencing data: GSE48307