GEO DataSets

(Submitter supplied) We applied previously designed array in order to widely cover all types of genes of 74 A. thaliana accessions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL14937

148 Samples

Download data: TXT

(Submitter supplied) Following previous work, we extend the use of a reliable detection method to a wide progeny in white spruce in order to genetically map a maximum of inherited gene CNVs and linked those to phenotypic traits related to adaptation. We selected probes targeting 3911 genes likely in CNV in this progeny and performed genetic mapping for those harboring a 1:1 segregation. In addition, the link between gene CNVs and phenotypic variation was tested using budburst, budset and growth data for the same samples. more...

Organism:

Picea glauca

Type:

Genome variation profiling by array

Platform:

GPL23818

115 Samples

Download data: TXT

(Submitter supplied) Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana. more...

Organism:

Arabidopsis lyrata; Arabidopsis halleri; Arabidopsis thaliana

Type:

Genome variation profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

176 Samples

Download data: CEL

(Submitter supplied) Gene copy-number variation, which provides the raw material for the evolution of novel genes, is surprisingly widespread in natural populations. Experimental evolution studies have demonstrated an extremely high spontaneous rate of origin of gene duplications. When organisms are suboptimally adapted to their environment, gene duplication may compensate for reduced fitness by amplifying promiscuous activity of a gene, or increasing dosage of a suboptimal gene. more...

Organism:

Caenorhabditis elegans

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL20029 GPL20028

45 Samples

Download data: PAIR, TXT

(Submitter supplied) Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. more...

Organism:

Bos taurus

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL18258

12 Samples

Download data: CEL, TXT

(Submitter supplied) This study used two different NimbleGen platforms to identify canine CNVs. The first identifies genome-wide CNVs while the second genotypes all known canine CNVs in a large panel of dogs from multiple breeds.

Organism:

Canis lupus; Canis lupus familiaris

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL11335 GPL11333

75 Samples

Download data: PAIR

(Submitter supplied) Novel, systems-based approach to mouse genetics.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8759

288 Samples

Download data: CEL

(Submitter supplied) Copy number variants (CNVs) affect both disease and normal phenotypic variation but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrate accurate estimation of absolute copy number for duplications as small as 1.9 kbp, ranging from 0-48 copies. We identified 4.1 million ‘singly unique nucleotide’ (SUN) positions informative in distinguishing specific copies, and use them to genotype the copy and content of specific paralogs within highly duplicated gene families. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10970

5 Samples

Download data: TXT

(Submitter supplied) Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL21785

728 Samples

Download data: TSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus domesticus; Mus spretus; Mus musculus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL11047 GPL10992

81 Samples

Download data: PAIR

(Submitter supplied) This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. more...

Organism:

Mus musculus; Mus spretus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11047

17 Samples

Download data: PAIR

(Submitter supplied) 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:

Mus musculus domesticus; Mus musculus; Mus spretus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10992

64 Samples

Download data: PAIR

(Submitter supplied) Copy number variation (CNV) of DNA segments has recently been identified as a major source of genetic diversity, but a more comprehensive understanding of the extent and phenotypic effect of this type of variation is only beginning to emerge. In this study we generated genome-wide expression data from 6 mouse tissues to investigate how CNVs influence gene expression. Keywords: genetic background, gene expression profiling

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

108 Samples

Download data: CEL

(Submitter supplied) 47,880 probe-sets were screened, in the first part of this study, they were analysed for correlation of transcripts levels with body composition traits

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL16569

297 Samples

Download data: CEL

(Submitter supplied) Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: CSV