Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide expression profiling analysis of a SMC6 mutant mouse model

ABSTRACT: The function of the SMC5-6 complex is less clear, but it has an important role in a variety of different DNA repair processes and in resolving recombination structures. Interestingly mutation at a highly conserved residue (Ser994) in the ATP hydrolysis motif in the SMC6 C-terminal domain, resulted in mice with a mild phenotype. Total RNA obtained from homozygote 4 male mutant mice was compared to 2-4 wild type or 2 heterozygote controls.

ORGANISM(S): Mus musculus

SUBMITTER: Marion Horsch

PROVIDER: E-GEOD-38737 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

SMC6 is an essential gene in mice, but a hypomorphic mutant in the ATPase domain has a mild phenotype with a range of subtle abnormalities.

Ju Limei L Wing Jonathan J Taylor Elaine E Brandt Renata R Slijepcevic Predrag P Horsch Marion M Rathkolb Birgit B Rácz Ildikó I Becker Lore L Hans Wolfgang W Adler Thure T Beckers Johannes J Rozman Jan J Klingenspor Martin M Wolf Eckhard E Zimmer Andreas A Klopstock Thomas T Busch Dirk H DH Gailus-Durner Valérie V Fuchs Helmut H de Angelis Martin Hrabě MH van der Horst Gilbertus G Lehmann Alan R AR

DNA repair 20130318 5

Smc5-6 is a highly conserved protein complex related to cohesin and condensin involved in the structural maintenance of chromosomes. In yeasts the Smc5-6 complex is essential for proliferation and is involved in DNA repair and homologous recombination. siRNA depletion of genes involved in the Smc5-6 complex in cultured mammalian cells results in sensitivity to some DNA damaging agents. In order to gain further insight into its role in mammals we have generated mice mutated in the Smc6 gene. A co ...[more]

PMID: 23518413

Similar Datasets

Genome-wide expression profiling analysis of a SMC6 mutant mouse model

Project description:The function of the SMC5-6 complex is less clear, but it has an important role in a variety of different DNA repair processes and in resolving recombination structures. Interestingly mutation at a highly conserved residue (Ser994) in the ATP hydrolysis motif in the SMC6 C-terminal domain, resulted in mice with a mild phenotype.

2013-04-22 | GSE38737 | GEO

Restless Legs Syndrome-associated variant in MEIS1 confers altered gene expression in embryonic ganglionic eminences

Project description:Genome-wide association studies (GWASs) identified the MEIS1 locus for Restless Legs Syndrome (RLS), but causal single nucleotide polymorphisms (SNPs) and the functional relevance have remained to be elucidated. The MEIS1 locus contains an exceptionally large number of highly conserved non-coding regions (HCNRs), which potentially function as cis-regulatory modules. We analyzed the HCNRs in the RLS-associated linkage disequilibrium (LD) block for allele-dependent enhancer activity in both zebrafish and mouse, comparing the protective and risk alleles of RLS-associated common variants. We found one enhancer, harboring the lead SNP rs12469063, which showed an allele-dependent reduction of reporter gene expression exclusively in the embryonic ganglionic eminences at developmental stage E12.5. Notably, the reporter activity overlapped with the endogenous telencephalic Meis1 expression domain, which co-localized with transcripts of all four validated RLS loci. Thus, the developing telencephalon represents the first neuroanatomic region implicated for RLS based on GWAS findings. Total RNA obtained from 2-3 male and female mice E12.5 (wildtype, heterzygote, homozygote) and 3-4 male heterozygote and wildtype mice (adult)

2014-01-29 | E-GEOD-44592 | biostudies-arrayexpress

Genome-wide expression profiling analysis of a Hmgn1, 3 and 5 mutant mouse model

Project description:Members of the HMGN protein family bind to nucleosomes and affect chromatin structure and functions as transcription, replication and DNA repair as well as epigenetic modifications. Overexpression of Hmgn1 may be linked to the etiology of Down syndrome while underexpression may be linked to some leukemias. Hmgn3 is highly expressed in eye and in brain and might influence behavioral phenotype. For Hmgn5 effects on transcription levels e.g. in liver are suggested. Total RNA obtained from four homozygote mutant and wildtype male mice were compared.

2013-07-03 | E-GEOD-39062 | biostudies-arrayexpress

Peroxidasin is essential for eye development

Project description:Within a mutatgenesis screen, we identified the new recessive mouse mutant KTA48 with a kinky tail, white spots on coat and with small eyes. Aim of the actual study was the molecular characterization of the mutant and the functional consequences of the mutation. We mapped the mutation to mouse chromosome 12 within a critical interval of 2.4 Mb between the markers D12Mit171 and D12Mit270; sequence analysis of Pxdn revealed a T->A mutation at position 3816 (T3816A) resulting in a premature stop codon (Cys1272X) in teh perosidasin domain. Histological analysis revealed variable, but severe defects in teh eye including all major ocular tissues (cornea, lens and retina). These findings demonstrate severe clinical findings of a recessive mutation affecting peroxidasin. Total RNA obtained from homozygote embryos E12.5 and wildtype embryos E12.5, each sample include 4 eyes of two embryos

2014-05-02 | E-GEOD-49704 | biostudies-arrayexpress

Genome-wide expression profiling analysis of the Ali35 mutant mouseline carrying a mutation in the Shc2 gene

Project description:Analysis of changes on gene expression levels in brain and bone for the linkage to phenotypical alterations found in behavior, neurology, nociception, bone remodelling and development. Total RNA isolated from bone and brain of Ali35 mutant mice compared to wildtype controls

2014-09-01 | E-GEOD-34079 | biostudies-arrayexpress

Decrease of Parkin and CD36 expression and body weight correlate with an increase of non-esterified fatty acids in a mouse model for TDP-43 pathology

Project description:TDP-43-coding mutations are found among ALS patients. In oder to express human mutant TDP-43 protein in the mouse under the control of the endogenous Tardp promoter, we have generate a mouse line wit 300% elevated TDP-43 level. Total RNA obtained from 4-6 male mutant mice was compared to 4-6 wild type controls.

2014-05-21 | E-GEOD-39585 | biostudies-arrayexpress

ENU derived mouse line AEA001: A model for osteoporosis carrying a mutation in Ednra

Project description:Transcriptome analysis of white adipose tissue and bone (femur of the hind limbs) of the AEA001 mutant mouse. ENU generated mouse lines for osteoporosis. The mutation in the Ednra gene causes big ears and a flat short head. Due to a decreased body mass and a trend towards decreased glucose level white adipose tissue was analysed. Total RNA obtained from 4 male mutant mice was compared to 4 controls.

2014-09-01 | E-GEOD-40428 | biostudies-arrayexpress

Mice lacking DUF1220 protein domains are hyperactive and show reduced fecundity

Project description:Sequences encoding DUF1220 protein domains show the most extreme human lineage-specific copy number increase of any coding region in the genome and have been linked to human brain evolution. In addition, DUF1220 copy number (dosage) has been implicated in influencing brain size within the human species, both in normal populations and in individuals associated with brain size pathologies (1q21-associated microcephaly and macrocephaly). More recently, increasing dosage of a subtype of DUF1220 has been linked with increasing severity of the primary symptoms of autism. Despite these intriguing associations, a function for these domains has not been described. As a first step in addressing this question we have developed the first transgenic model of DUF1220 function by removing the single DUF1220 domain (the ancestral form) encoded in the mouse genome. While resulting DUF1220-minus (KO) mice show no obvious anatomical peculiarities, they exhibit a significantly reduced fecundity (χ2= 19.1, df = 2, p = 7.0 x 10-5). Further extensive phenotypic analyses suggest that DUF1220 KO mice are hyperactive (p < 0.05) relative to wild type litter mates. The linking of DUF1220 loss to a hyperactive phenotype is consistent with separate findings in which DUF1220 over expression results in a down-regulation of mitochondrial function, suggesting a possible role in the prolongation of developmental processes (neoteny) that is most pronounced in the human lineage. Total RNA obtained from brain of 3 male homozygous Duf1220 ko and 4 male wildtype mice

2014-09-22 | E-GEOD-58308 | biostudies-arrayexpress

Jag1K295*/+ as a mouse model for Alagille syndrome

Project description:A new mouse mutant was identified at the Munich ENU mutagenesis project due to hyperactivity, head tossing, and circling behaviour. Neurological and gross morphological phenotyping of these mutant mice revealed impairment of the vestibular system. Using whole genome exome sequencing and a custom-made variant calling pipeline, we identified the causative mutation as an A->T substitution on the chromosome 2 at the position 128 in the exon 6 of jagged 1 (Jag1) gene. This introduces a premature termination codon at the position 883 of the cDNA. In humans, mutations in the JAG1 gene are associated with Alagille syndrome (ALGS1 ), a multisystem developmental disorder mainly affecting small bile ducts in the liver, but also heart, skeleton, and eyes, and occasionally also kidney or inner ears. Further examination of the Jag1K295*/+ mutant mouse line disclosed multiorgan deficiencies, such as cardiac liver congestion, bile duct hypoplasia, mild nephropathy, subvalvular hypertrophy of the right ventricle, and mild growth retardation. No skeletal abnormalities could be detected. In summary, we report a novel mouse model for Alagille syndrome, Jag1K295*/+, which resembles most of the features of the mild form of Alagille syndrome observed in patients. Total RNA obtained from liver of 4 male heterozygous Jag1K295*/+ and 4 male wildtype mice

2014-10-01 | E-GEOD-55602 | biostudies-arrayexpress

IFIT2 mediates IFN signaling

Project description:IFit2 is highly induced in response to type I and type II interferons, dsRNA, LPS, viral and bacterial infections and it is als found in several chronic diseases.A possible role for the protein in cell proliferation, virion assembly/transport and microtubule dynamices was described. This study focus on IFIT2 proinflammatory cytokine response which might be involved in the development of septic shock. In the IFIT2 knockout mice gene expression levels before and after OVA challenge were analysed. Total RNA obtained from 3-4 male mutant mice (challenged/un-challenged) was compared to 4 wild type controls (challenged/unchallenged).

2014-05-02 | E-GEOD-39953 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data