Transcriptomics

Dataset Information

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RNA-Seq characterization of select lincRNA knockout mouse models


ABSTRACT: It has become clear that long intergenic noncoding RNAs (lincRNAs) are an important layer of genome regulation. Thousands have been identified in mammals, yet only a few have been tested through genetic ablation in animal models. Of the few that have, many yields weak to unobservable phenotypes, raising the question of their in vivo relevance. To more broadly investigate the functional relevance of lincRNAs in physiological conditions, we developed a collection of 18 lincRNA knockout strains. We found that two knockout strains, linc-Sox2 and linc-Foxf1a (Fendrr), exhibit perinatal lethal phenotypes in addition to multiple developmental abnormalities. Notably, in depth analysis of a third mutant strain, linc-Brn1b-/-, revealed defects in brain development, with distinct abnormalities in class-specific generation of upper layer II/III-IV neurons in the neocortex. Thus far, we found at least 6 of 18 mutant strains exhibit distinct developmental or lethality phenotypes. Therefore, this study demonstrates that lincRNAs are required for life and play critical roles during mammalian development, highlighting the importance of studying them further to better understand the molecular mechanisms leading to disease. Minimum 2 replicates each of select wild type and lincRNA knockout embryonic and postnatal tissues for three distinct lincRNA knockout mouse strains.

ORGANISM(S): Mus musculus  

SUBMITTER: Chiara Gerhardinger   Abigail F Groff  Matthew Spence  John L Rinn  Guochun Gong  David M Valenzuela  Mavis Swerdel  David Frendewey  Loyal A Goff  Diana B Sanchez  Martin Sauvageau  Manolis Kellis  Ezgi Hacisuleyman  Michael D'Ecclessis  George D Yancopoulos  Boyan Bonev  Simona Lodato  Venus Lai  Eric Li  Paola Arlotta  Jennifer C Moore  Ronald P Hart 

PROVIDER: E-GEOD-49581 | ArrayExpress | 2013-11-30

SECONDARY ACCESSION(S): SRP028547GSE49581PRJNA214363

REPOSITORIES: GEO, ArrayExpress, ENA

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