Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Copy number variation in inbred and wild mice

ABSTRACT: Copy number variants were determined in 3-5 males from 13 inbred laboratory mouse strains and 21 Mus musculus individuals caught in various geographic locations, using Nimblegen 385k arrays. CopyMap was used to predict CNVs.

ORGANISM(S): Mus musculus Mus musculus domesticus Mus spretus

PROVIDER: GSE24424 | GEO | 2010/12/31

SECONDARY ACCESSION(S): PRJNA133505

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Copy number variation in inbred and wild mice

Project description:Copy number variants were determined in 3-5 males from 13 inbred laboratory mouse strains and 21 Mus musculus individuals caught in various geographic locations, using Nimblegen 385k arrays. CopyMap was used to predict CNVs. 3-5 males from 13 inbred strains and 21 Mus musculus caught in various geographic locations were compared to a single C57BL/6J individual by array comparative genome hybridisation.

2010-12-31 | E-GEOD-24424 | biostudies-arrayexpress

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

Project description:Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1,000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the lower signal:noise ratio inherent in oligonucleotide-based hybridization assays. We have developed wuHMM, an algorithm for mapping CNVs from array comparative genomic hybridization (aCGH) platforms comprised of 385,000 to more than 3 million probes. wuHMM is unique in that it can utilize sequence divergence information to reduce the false positive rate (FPR). We apply wuHMM to 385K-aCGH, 2.1M-aCGH, and 3.1M-aCGH experiments comparing the 129X1/SvJ and C57BL/6J inbred mouse genomes. We assess wuHMM’s performance on the 385K platform by comparison to the higher resolution platforms and we independently validate 10 CNVs. The method requires no training data and is robust with respect to changes in algorithm parameters. At a FPR of less than 10%, the algorithm can detect CNVs with five probes on the 385K platform and three on the 2.1M and 3.1M platforms, resulting in effective resolutions of 24 kb, 2-5 kb, and 1 kb, respectively. Keywords: CNV detection algorithm development and assessment

2008-03-12 | GSE10511 | GEO

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

2008-03-11 | E-GEOD-10511 | biostudies-arrayexpress

Variation in mouse chemical signals is genetically controlled and environmentally modulated

Project description:Urine proteomes of the house mouse (Mus musculus musculus, M. m. domesticus, M. m. castaneus).

2023-07-20 | PXD037086 | Pride

Testis expression in Mus musculus domesticus x Mus musculus musculus hybrid zone mice

Project description:We collected whole genome testis expression data from hybrid zone mice. We integrated GWAS mapping of testis expression traits and low testis weight to gain insight into the genetic basis of hybrid male sterility. Gene expression was measured in whole testis from males aged 62-86 days. Samples include 190 first generation lab-bred male offspring of wild-caught mice from the Mus musculus musculus - M. m. domesticus hybrid zone.

2014-12-04 | E-GEOD-61417 | biostudies-arrayexpress

Mus musculus breed:Inbred Long Sleep (ILS), Inbred Short Sleep (ISS)

Project description:Mus musculus breed:Inbred Long Sleep (ILS), Inbred Short Sleep (ISS) Raw sequence reads

| PRJNA353308 | ENA

Contrasting patterns of expression divergence in early and late stages of population divergence in mice

Project description:We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis. Keywords: multi-species comparison

2006-12-13 | GSE2597 | GEO

An initial map of chromosomal segmental copy number variations in chickens

Project description:Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits.

2010-06-11 | GSE19469 | GEO

Mouse Inbred Strain Variation Muscle

Project description:Variation in gene expression profiles was determined between mouse inbred strains in hindlimb muscle tissue. Strains under investigation were: C57Bl/6, C57Bl/10, CBA, DBA2, and BALB/c. Keywords: other

2003-12-10 | GSE662 | GEO

Mus musculus strain:C57BL/6J | breed:inbred

Project description:Mus musculus strain:C57BL/6J | breed:inbred Raw sequence reads

| PRJNA470690 | ENA