GEO DataSets

(Submitter supplied) Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. more...

Organism:

Zea mays subsp. parviglumis; Zea mays

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10846

58 Samples

Download data: PAIR

(Submitter supplied) Following the domestication of maize over the past 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. more...

Organism:

Zea mays

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8790

9 Samples

Download data: PAIR, TXT

(Submitter supplied) Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. more...

Organism:

Zea mays

Type:

Methylation profiling by genome tiling array

Platform:

GPL13499

3 Samples

Download data: PAIR, TXT

(Submitter supplied) Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we assessed allele-specific expression in a collection of maize and teosinte inbreds and their F1 hybrids using three tissues from different developmental stages. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

448 Samples

Download data: TXT

(Submitter supplied) The contribution of epigenetic alterations to natural variation for gene transcription levels remains unclear. In this study, we investigated the functional targets of the maize chromomethylase ZMET2 in multiple inbred lines to determine whether epigenetic changes conditioned by this chromomethylase are conserved or variable within the species. Gene expression microarrays were hybridized with RNA samples from the inbred lines B73 and Mo17, and from near-isogenic derivatives containing the loss-of-function allele zmet2-m1. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

18 Samples

Download data: CEL, CHP

(Submitter supplied) We have generated over 80 million 32 nt reads generated from RNA samples isolated from the tip and base of a developing Mo17 leaf. A comparision of these data with the maize AGP resulted in the confirmation of approximately 88% of the maize filtered gene set Keywords: Transcriptome analysis

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9361

2 Samples

Download data: TXT

(Submitter supplied) All above ground organs of higher plants are ultimately derived from shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, and monocot SAMs such as maize are comprised of two cell layers, a single cell layered tunica (L1) and a corpus (L2). Although recent research has revealed roles of these cell layers in the SAM, intra- and inter-cell-layer signaling networks involved in organ development remain largely unknown except for a few differentially expressed genes. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9141

2 Samples

Download data: TXT

(Submitter supplied) Heterosis (hybrid vigor) refers to the superior performance of hybrid progeny relative to their parents. Although widely exploited in agriculture, the mechanisms responsible for heterosis are not well understood. As a monoecious organism, a given maize plant can be used as both male and female parents of crosses. Regardless of the cross direction, the maize inbred lines B73 and Mo17 produce hybrids that substantially out-perform their parents. more...

Organism:

Zea mays

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

533 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) DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, other genetic changes such as transposon insertions also can lead to changes in DNA methylation levels. Genome-wide profiles of DNA methylation levels for 20 maize inbreds were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize genotypes resulting in the discovery of 1,966 common DMRs and 1,754 rare DMRs. more...

Organism:

Zea mays

Type:

Methylation profiling by genome tiling array

Platforms:

GPL17181 GPL15621 GPL13499

86 Samples

Download data: PAIR

(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) The Goto-Kakizak (GK) rat, a nonobese animal model of Type 2 diabetes (T2D), were developed by repeated inbreeding of glucose-intolerent individuals selected from Wistar rats. During their development, GK rats suffer from reduced beta-cell mass and insulin resistance spontaneously (T2D phenotype), which are supposed to be caused by loci holding different genotypes between GK and Wistar rats. This array CGH experiment can detect loci which show different copy numbers (genotype) between GK and Wistar rats. more...

Organism:

Rattus norvegicus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10340

3 Samples

Download data: TXT

(Submitter supplied) Somatic tissues were hybridized against a reference tissue selected for each subject. Two hybridizations were performed for each tissue comparison (regular and dye-swap)

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL13190

52 Samples

Download data: PAIR, TXT