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Series GSE49581 Query DataSets for GSE49581
Status Public on Nov 30, 2013
Title RNA-Seq characterization of select lincRNA knockout mouse models
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design Minimum 2 replicates each of select wild type and lincRNA knockout embryonic and postnatal tissues for three distinct lincRNA knockout mouse strains.
Contributor(s) Goff LA, Sauvageau M, Lodato S, Bonev B, Groff AF, Sanchez DB, Gerhardinger C, Hacisuleyman E, Li E, Spence M, Swerdel M, D'Ecclessis M, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL
Citation(s) 24381249
Submission date Aug 06, 2013
Last update date May 15, 2019
Contact name Loyal A Goff
Organization name Johns Hopkins University
Department Institute of Genetic Medicine
Lab Goff
Street address 733 N. Broadway Avenue
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (21)
GSM1202232 lincSox2_E18-5_Brain_46WT
GSM1202233 lincSox2_E18-5_Brain_48WT
GSM1202234 lincSox2_E18-5_Brain_28KO
BioProject PRJNA214363
SRA SRP028547

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