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accession-icon GSE8194
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression
  • organism-icon Zea mays
  • sample-icon 36 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-8194

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8174
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling data
  • organism-icon Zea mays
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-8174

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8179
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Embryo data
  • organism-icon Zea mays
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-8179

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8176
Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data
  • organism-icon Zea mays
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-8176

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8308
Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP and 19DAP
  • organism-icon Zea mays
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-8308

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8278
Non-additive and imprinted gene expression in hybrid maize endosperm_19DAP
  • organism-icon Zea mays
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-8278

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8275
Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP
  • organism-icon Zea mays
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-8275

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE10243
Profiling expression changes caused by a segmental aneuploid in maize
  • organism-icon Zea mays
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Maize Genome Array (maize)

Description

ABSTRACT: BACKGROUND: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that ~40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage. CONCLUSIONS: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions.

Publication Title

Profiling expression changes caused by a segmental aneuploid in maize.

Alternate Accession IDs

E-GEOD-10243

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE10236
Similar patterns of additive and non-additive gene expression in maize hybrids with varying levels of heterosis
  • organism-icon Zea mays
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-10236

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE10237
Gene expression variation among eight maize inbreds
  • organism-icon Zea mays
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon 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.

Alternate Accession IDs

E-GEOD-10237

Sample Metadata Fields

No sample metadata fields

View Samples
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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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