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GSE16119
Homo sapiens
2 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Little is known about the immune performance and interactions of CNS microglia/macrophages in glioma patients. Microglia/macrophages were found to be the predominant immune cell infiltrating gliomas (approximately 1% of total cells); others identified are myeloid dendritic cells (DCs), plasmacytoid DCs, and T cells. Using a procedure enriching for CD11b/c+CD45+ glioma-infiltrating microglia/macrophages (GIMs) from postoperative tissue specimens of glioma patients (Hussain et al. Neuro Oncol. 2006 J;8(3):261-79) gene expression profiles were obtained form paired samples. The expression profiles are used to identify expression signatures contributed by GIMs in glioblastoma data sets (Murat et al, submitted).
Publication Title
Modulation of angiogenic and inflammatory response in glioblastoma by hypoxia.
Sample Metadata Fields
Sex, 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- Zea mays
- 27 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
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. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range. These findings indicate that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines.
Publication Title
Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 24 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. Many genes exhibit presence-absence variation among the inbred lines.
Publication Title
Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.
Sample Metadata Fields
No sample metadata fields
View Samples