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E-GEOD-41338 - RNA-seq of poly-A enriched total RNA of brain, liver, kidney, heart and skeletal muscle samples from 5 vertebrate species: mouse, chicken, frog, lizard and pufferfish

Status
Released on 22 December 2012, last updated on 30 April 2015
Organism
Anolis carolinensis, Gallus gallus, Mus musculus, Tetraodon nigroviridis, Xenopus tropicalis
Samples (21)
Protocols (2)
Description
How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species. mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq
Experiment type
RNA-seq of coding RNA 
Contacts
Nuno L Barbosa-Morais <nuno.barbosa.morais@utoronto.ca>, Benjamin J Blencowe, Claudia Kutter, Duncan T Odom, Stephen Watt
Citation
The evolutionary landscape of alternative splicing in vertebrate species. Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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