GEO DataSets

(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) Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. A wealth of archeological and population genetic data has established maize as a model system for studying domestication , genome evolution and the genetics and evolution of complex traits. We used expression profiling of 18,242 genes for 38 diverse maize genotypes and 18 teosinte genotypes to examine how domestication has re-shaped the transcriptome of maize seedlings. more...

Organism:

Zea mays; Zea mays subsp. parviglumis

Type:

Expression profiling by array

Platform:

GPL13736

94 Samples

Download data: PAIR

(Submitter supplied) DNA methylation is a ubiquitous chromatin feature — in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea mays ssp. more...

Organism:

Zea mays

Type:

Other; Methylation profiling by high throughput sequencing

Platforms:

GPL15463 GPL17628

74 Samples

Download data: BED, XLS

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

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

36 Samples

Download data: CEL, CHP

(Submitter supplied) Microarray analysis of gene expression patterns in immature ear, seedling, and embryo tissues from the maize inbred lines B73 and Mo17 identified numerous genes with variable expression. Some genes had detectable expression in only one of the two inbreds; most of these genes were detected in the genomic DNA of both inbreds, indicating that the expression differences are likely caused by differential regulation rather than by differences in gene content. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

12 Samples

Download data: CEL, CHP

(Submitter supplied) Microarray analysis of gene expression patterns in immature ear, seedling, and embryo tissues from the maize inbred lines B73 and Mo17 identified numerous genes with variable expression. Some genes had detectable expression in only one of the two inbreds; most of these genes were detected in the genomic DNA of both inbreds, indicating that the expression differences are likely caused by differential regulation rather than by differences in gene content. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

12 Samples

Download data: CEL, CHP

(Submitter supplied) Microarray analysis of gene expression patterns in immature ear, seedling, and embryo tissues from the maize inbred lines B73 and Mo17 identified numerous genes with variable expression. Some genes had detectable expression in only one of the two inbreds; most of these genes were detected in the genomic DNA of both inbreds, indicating that the expression differences are likely caused by differential regulation rather than by differences in gene content. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

12 Samples

Download data: CEL, CHP

(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) Using RNA-seq technology, a comprehensive assessment of cis regulatory divergence in interspecific hybrid female heads was conducted and patterns of sequence evolution (Begun et al. 2007) within causal loci were examined. Genotype specific references were shown to virtually eliminate the map bias plaguing this technology. A novel Bayesian model, which uses allele representation in F1 hybrid DNA sequence reads as a prior, was used to estimate allele frequencies in RNA sequences.

Organism:

Drosophila melanogaster x Drosophila simulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15045

3 Samples

Download data: CSV

(Submitter supplied) The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20156

2 Samples

Download data: BED, TXT

(Submitter supplied) The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. more...

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: TXT

(Submitter supplied) Chromatin accessibility and modification is a hallmark of regulatory DNA, which has led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants especially in species with large and complex genomes. more...

Organism:

Arabidopsis thaliana; Phaseolus vulgaris; Sorghum bicolor; Zea mays; Spirodela polyrhiza; Oryza sativa; Brachypodium distachyon; Populus trichocarpa; Glycine max; Hordeum vulgare; Setaria viridis; Asparagus officinalis; Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

13 related Platforms

170 Samples

Download data: BW

(Submitter supplied) Genetic mapping studies on crops suggest that agronomic traits can be controlled by loci within the gene-distal intergenic space. Despite the biological importance and the potential agronomic utility of these intergenic loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic, and functional molecular evidence supporting the widespread existence of gene-distal (hereafter, distal) loci which act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL17628 GPL20156

81 Samples

Download data: BED, TSV, TXT

(Submitter supplied) Cis-regulatory elements (CREs) encode the genomic blueprints for coordinating the spatiotemporal regulation of gene transcription programs necessary for highly specialized cellular functions. To identify cis-regulatory elements underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in an atlas of Zea mays tissues and organs. more...

Organism:

Arabidopsis thaliana; Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26208 GPL25410

14 Samples

Download data: TXT

(Submitter supplied) Gene regulation can evolve either by cis-acting local changes to regulatory element DNA sequences or by global changes to the trans-acting regulatory environment; however, the modes favored during recent human evolution are unknown. To date, studies investigating gene regulatory divergence between closely-related species have produced limited estimates on the relative contributions of cis and trans effects on DNA regulatory element activities at a global-scale. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL32794 GPL24676 GPL27943

22 Samples

Download data: BED, BW, TSV

(Submitter supplied) Massively parallel reporter assays (MPRAs) test the capacity of putative gene regulatory elements to drive transcription on a genome-wide scale. Most gene regulatory activity occurs within accessible chromatin, and recently described methods have combined assays that capture these regions—such as assay for transposase-accessible chromatin using sequencing (ATAC-seq)—with self-transcribing active regulatory region sequencing (STARR-seq) to selectively assay the regulatory potential of accessible DNA (ATAC-STARR-seq). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL24676

7 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) These data were generated in a study to analyze the genetic causes of gene regulatory divergence. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion, "D_mel_x_D_sec"). A mixed mRNA- seq library was prepared from D. melanogaster and D. sechellia poly(A) + RNA (mixed before library preparation, "D_mel_+_D_sec). more...

Organism:

Drosophila sechellia; Drosophila melanogaster x Drosophila sechellia; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: BED

(Submitter supplied) To ascertain whether ZmCCT is involved in the development of anther.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

18 Samples

Download data: TAB, TXT

(Submitter supplied) A fundamental challenge in genomics is to map DNA sequence variants onto changes in gene expression. Gene expression is regulated by cis-regulatory elements (CREs, i.e., enhancers, promoters, and silencers) and the trans factors (e.g., transcription factors) that act upon them. A powerful approach to dissecting cis and trans effects is to compare F1 hybrids with F0 homozygotes. Using this approach and taking advantage of the high frequency of polymorphisms in wild-derived inbred Cast/EiJ mice relative to the reference strain C57BL/6J, we conducted allele-specific mRNA-seq analysis in the adult mouse retina, a disease-relevant neural tissue. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans activating factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we investigate the global patterns of gene expression evolution in Saccharomyces cerivisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9134

24 Samples

Download data: TXT