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Links from GEO DataSets

Items: 20

1.

Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP

(Submitter supplied) The nuclear content of the plant endosperm is the result of the contribution two maternal genomes and a single paternal genome. This 2:1 dosage relationship provides a unique system for studying the additivity of gene expression levels in reciprocal hybrids. A combination of microarray profiling and allele-specific expression analysis was performed using RNA isolated from endosperm tissues of maize inbred lines B73 and Mo17 and their reciprocal hybrids at two developmental stages, 13 and 19 days after pollination. more...
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL4032
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE8275
ID:
200008275
2.

Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP and 19DAP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL4032
24 Samples
Download data: CEL, CHP
Series
Accession:
GSE8308
ID:
200008308
3.

Non-additive and imprinted gene expression in hybrid maize endosperm_19DAP

(Submitter supplied) The nuclear content of the plant endosperm is the result of the contribution two maternal genomes and a single paternal genome. This 2:1 dosage relationship provides a unique system for studying the additivity of gene expression levels in reciprocal hybrids. A combination of microarray profiling and allele-specific expression analysis was performed using RNA isolated from endosperm tissues of maize inbred lines B73 and Mo17 and their reciprocal hybrids at two developmental stages, 13 and 19 days after pollination. more...
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL4032
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE8278
ID:
200008278
4.

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression

(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
Series
Accession:
GSE8194
ID:
200008194
5.

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Embryo data

(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
Series
Accession:
GSE8179
ID:
200008179
6.

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data

(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
Series
Accession:
GSE8176
ID:
200008176
7.

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling data

(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
Series
Accession:
GSE8174
ID:
200008174
8.

Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm Development

(Submitter supplied) In angiosperms, the endosperm provides nutrients for embryogenesis or seed germination and is the primary tissue where gene imprinting occurs. To map the imprintome of the early developing endosperm in maize, we performed high-throughput transcriptome sequencing of the kernels at 0, 3, 5 days after pollination (DAP) and the endosperms at 7, 10, and 15 DAP produced from the B73 and Mo17 reciprocal crosses. more...
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15463
12 Samples
Download data: TXT
Series
Accession:
GSE48425
ID:
200048425
9.

Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm

(Submitter supplied) Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). more...
Organism:
Zea mays
Type:
Methylation profiling by genome tiling array
Platform:
GPL13499
6 Samples
Download data: PAIR, TXT
Series
Accession:
GSE33730
ID:
200033730
10.

Regulation of Gene Expression and Parent-of-Origin Effects in Maize Hybrids

(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
Series
Accession:
GSE16136
ID:
200016136
11.

Sequential gene activation and extensive gene imprinting during early embryo development in maize

(Submitter supplied) The embryo is responsible for transmitting genetic information to the next generation. However, the underlying gene expression and gene imprinting during early embryo development remain largely elusive in maize. Using high-throughput RNA sequencing, we analyzed the allelic gene expression patterns of maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3 to 13 days after pollination). more...
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17628
48 Samples
Download data: XLS
Series
Accession:
GSE95399
ID:
200095399
12.

Maize primary roots: inbred lines vs. hybrids

(Submitter supplied) The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. more...
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL1996
168 Samples
Download data: TXT
Series
Accession:
GSE10539
ID:
200010539
13.

Expression profiling of zmet2-m1 mutants relative to wild-type

(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
Series
Accession:
GSE8188
ID:
200008188
14.

Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

(Submitter supplied) Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups. There are numerous differences in the distribution of H3K27me3 among tissues. more...
Organism:
Zea mays
Type:
Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL15621 GPL13499
13 Samples
Download data: PAIR
Series
Accession:
GSE39456
ID:
200039456
15.

Imprinted expression of genes and small RNA is triggered by localized demethylation of the maternal genome in rice endosperm

(Submitter supplied) We report that rice endosperm shows a specific hypomethylation of DNA in the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. more...
Organism:
Oryza sativa
Type:
Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL13160 GPL15432
16 Samples
Download data: GFF
Series
Accession:
GSE44898
ID:
200044898
16.

Gene expression variation among eight maize inbreds - 70mer oligo array

(Submitter supplied) Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10237). Keywords: Genotype comparison series
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL6438
24 Samples
Download data: GPR
Series
Accession:
GSE10543
ID:
200010543
17.

Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis - 70mer

(Submitter supplied) Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236). Keywords: Genotype comparison series
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL6438
27 Samples
Download data: GPR
Series
Accession:
GSE10542
ID:
200010542
18.

Gene expression variation among eight maize inbreds

(Submitter supplied) Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. Many genes exhibit presence-absence variation among the inbred lines. Keywords: Genotype comparison series
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL4032
24 Samples
Download data: CEL, CHP
Series
Accession:
GSE10237
ID:
200010237
19.

Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis

(Submitter supplied) Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. more...
Organism:
Zea mays
Type:
Expression profiling by array
Platform:
GPL4032
27 Samples
Download data: CEL, CHP
Series
Accession:
GSE10236
ID:
200010236
20.

The naked endosperm genes encode duplicate ID domain transcription factors required for maize endosperm differentiation

(Submitter supplied) The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm developent. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology.
Organism:
Zea mays
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17628
12 Samples
Download data: TXT
Series
Accession:
GSE61057
ID:
200061057
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