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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| Overall design |
Minimum 2 replicates each of select wild type and lincRNA knockout embryonic and postnatal tissues for three distinct lincRNA knockout mouse strains.
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| 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 |
| E-mail(s) |
loyalgoff@jhmi.edu
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| Organization name |
Johns Hopkins University
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| Department |
Institute of Genetic Medicine
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| Lab |
Goff
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| Street address |
733 N. Broadway Avenue
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA214363 |
| SRA |
SRP028547 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE49581_lincBrn1b_All_timepoints_cuffdiff.tab.gz |
7.2 Mb |
(ftp)(http) |
TAB |
| GSE49581_lincFoxf1a_E14.5_Lung_cuffdiff.tab.gz |
1.3 Mb |
(ftp)(http) |
TAB |
| GSE49581_lincSox2_E18.5_Brain_cuffdiff.tab.gz |
1.3 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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