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Mus musculus
112 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Growth and patterning of the face relies on several small buds of tissue, the facial prominences, which surround the primitive mouth. Beginning around E10 of mouse development the prominences undergo rapid growth and morphogenesis. By E11.5 the medial nasal prominences are in close apposition in the midline, as are the maxillary and medial nasal prominences on either side of the developing face. Subsequently, by E12.5 the nasal and maxillary prominences fuse to form a continuous shelf at the front of the face - the primary palate. Individual prominences are associated with specific developmental processes, and this is reflected by patterns of differential gene expression that give the prominences their unique identities. Thus, only the mandibular and maxillary prominences give rise to dentition while the frontonasal prominence has a unique role in olfaction, and the mandibular prominence in taste. We used microarrays to detail the differential gene expression program in each of the mandibular, maxillary, and frontonasal prominences during the key developmental timepoints of E10.0 through E12.5.
Publication Title
Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 45 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This investigation provides a robust multi-dimensional compendium of gene expression data relevant to mouse facial development. It profiles the transcriptome ofectoderm and mesenchyme from the three facial prominences in a time series encompassing their growth and fusion. Analysis of the dataset identified more than 8000 differentially expressed genes comprising dramatically different ectoderm and mesenchyme programs. The mesenchyme programs included many genes identified in earlier analyses as well hundreds of genes not previously implicated in craniofacial development. The ectoderm programs included over a thousand genes that highlight epithelial structure, cell-cell interactions and signaling.
Publication Title
Systems biology of facial development: contributions of ectoderm and mesenchyme.
Sample Metadata Fields
Specimen part
View Samples
GSE60058- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Neo/null loss of Tfap2a in E10.5 mouse facial prominences
Publication Title
Tfap2a-dependent changes in mouse facial morphology result in clefting that can be ameliorated by a reduction in Fgf8 gene dosage.
Sample Metadata Fields
Specimen part
View Samples- Zea mays
- 36 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid.
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 12 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
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. Gene expression was also monitored in the reciprocal F1 hybrids B73xMo17 and Mo17xB73. The reciprocal F1 hybrid lines did not display parental effects on gene expression levels. Approximately 80% of the differentially expressed genes displayed additive expression patterns in the hybrids relative to the inbred parents. The approximately 20% of genes that display nonadditive expression patterns tend to be expressed at levels within the parental range, with minimal evidence for novel expression levels greater than the high parent or less than the low parent. Analysis of allele-specific expression patterns in the hybrid suggested that intraspecific variation in gene expression levels is largely attributable to cis-regulatory variation in maize. Collectively, our data suggest that allelic cis-regulatory variation between B73 and Mo17 dictates maintenance of inbred allelic expression levels in the F1 hybrid, resulting in additive expression patterns.
Publication Title
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid.
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 12 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
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. Gene expression was also monitored in the reciprocal F1 hybrids B73xMo17 and Mo17xB73. The reciprocal F1 hybrid lines did not display parental effects on gene expression levels. Approximately 80% of the differentially expressed genes displayed additive expression patterns in the hybrids relative to the inbred parents. The approximately 20% of genes that display nonadditive expression patterns tend to be expressed at levels within the parental range, with minimal evidence for novel expression levels greater than the high parent or less than the low parent. Analysis of allele-specific expression patterns in the hybrid suggested that intraspecific variation in gene expression levels is largely attributable to cis-regulatory variation in maize. Collectively, our data suggest that allelic cis-regulatory variation between B73 and Mo17 dictates maintenance of inbred allelic expression levels in the F1 hybrid, resulting in additive expression patterns.
Publication Title
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid.
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 12 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
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. Gene expression was also monitored in the reciprocal F1 hybrids B73xMo17 and Mo17xB73. The reciprocal F1 hybrid lines did not display parental effects on gene expression levels. Approximately 80% of the differentially expressed genes displayed additive expression patterns in the hybrids relative to the inbred parents. The approximately 20% of genes that display nonadditive expression patterns tend to be expressed at levels within the parental range, with minimal evidence for novel expression levels greater than the high parent or less than the low parent. Analysis of allele-specific expression patterns in the hybrid suggested that intraspecific variation in gene expression levels is largely attributable to cis-regulatory variation in maize. Collectively, our data suggest that allelic cis-regulatory variation between B73 and Mo17 dictates maintenance of inbred allelic expression levels in the F1 hybrid, resulting in additive expression patterns.
Publication Title
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid.
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 24 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm.
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 12 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
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. By assessing the relative levels of expression in the reciprocal hybrids it was possible to determine the prevalence of additive and non-additive expression patterns. While the majority of differentially expressed genes displayed additive expression patterns in the endosperm, approximately 10% of the genes displayed non-additive expression patterns including maternal-like, paternal-like, dominant high-parent, dominant low-parent and expression patterns outside the range of the inbreds. The frequency of hybrid expression patterns outside of the parental range in maize endosperm tissue is much higher than that observed for vegetative tissues. For a set of 90 genes allele-specific expression assays were employed to monitor allelic bias and regulatory variation. Eight of these genes exhibited evidence for maternally or paternally biased expression at multiple stages of endosperm development and are potential examples of differential imprinting. Collectively, our data indicate that parental effects on gene expression are much stronger in endosperm than in vegetative tissues, and that endosperm imprinting may be far more common than previously estimated.
Publication Title
Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm.
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 12 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
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. By assessing the relative levels of expression in the reciprocal hybrids it was possible to determine the prevalence of additive and non-additive expression patterns. While the majority of differentially expressed genes displayed additive expression patterns in the endosperm, approximately 10% of the genes displayed non-additive expression patterns including maternal-like, paternal-like, dominant high-parent, dominant low-parent and expression patterns outside the range of the inbreds. The frequency of hybrid expression patterns outside of the parental range in maize endosperm tissue is much higher than that observed for vegetative tissues. For a set of 90 genes allele-specific expression assays were employed to monitor allelic bias and regulatory variation. Eight of these genes exhibited evidence for maternally or paternally biased expression at multiple stages of endosperm development and are potential examples of differential imprinting. Collectively, our data indicate that parental effects on gene expression are much stronger in endosperm than in vegetative tissues, and that endosperm imprinting may be far more common than previously estimated.
Publication Title
Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm.
Sample Metadata Fields
No sample metadata fields
View Samples