Ontology highlight
ABSTRACT:
PROVIDER: PRJNA623806 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11509903_1.fastq.gz | Fastqsanger.gz | |||
| SRR11509903_2.fastq.gz | Fastqsanger.gz | |||
| SRR11509904_1.fastq.gz | Fastqsanger.gz | |||
| SRR11509904_2.fastq.gz | Fastqsanger.gz | |||
| SRR11509905_1.fastq.gz | Fastqsanger.gz |
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Project description:Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. To investigate the allele-specific DNA methylation pattern of maize endosperm on a genome-wide scale, we performed MethylC-seq for shoot, embryo, and endosperm tissue 12 d after pollination (DAP) of inbred B73, and the endosperm tissue 12 DAP of reciprocal crosses B73 Ã Mo17 (BM) and Mo17 Ã B73 (MB). We also performed additional RNA-seq for samples from 12-DAP and 10-DAP endosperm of both reciprocal crosses between inbreds B73 and Mo17
2013-10-17 | E-MTAB-4206 | biostudies-arrayexpress
Project 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. Experiment Overall Design: Gene expression levels were profiled in 19 day after pollination endosperm tissue from four maize genotypes; B73, Mo17, Mo17xB73 and B73xMo17.
2008-06-16 | E-GEOD-8278 | biostudies-arrayexpress
Project 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. Experiment Overall Design: Affymetrix microarrays were used to perform expression profiling on 13 day after pollination endosperm tissue of four different genotypes; B73; Mo17, B73xMo17 and Mo17xB73. There are three biological replicates for each of the tissues. Each biological sample represents a pool containing 5 endosperms each, from 6 different ears.
2008-06-16 | E-GEOD-8275 | biostudies-arrayexpress
Project description:Reciprocal crosses of a diploid Arabidopsis with different ploidies results in different endosperm development patterns and phenotype. Typically if the ploidy is higher on the maternal side, there are fewer endosperm cells which cellularize early, and conversely, if the paternal ploidy is higher, there is more number of endosperm cells which cellularize late. Crosses involving diploid and tetraploid Arabidopsis (C24) are viable, whereas crosses involving the diploid and hexaploid, even though exhibit the above mentioned directional trend in endosperm development, abort (Scott et al 1998). The 'maternalised' and 'paternalised' development of endosperm is also observed in crosses involving some Arabidopsis mutants. Mutants in the fis class of genes, e.g. fis1-medea, when crossed with a diploid Arabidopsis (pollen parent) show endosperm development-seed development similar to a diploid (seed parent) crossed with hexaploid pollen parent. Reciprocal crosses of homozygous met1 and diploid Arabidopsis also exhibit reciprocal trends in endosperm development, where a homozygous met1 mutant (seed parent) crossed with diploid is similar in phenotype to a diploid (seed parent) - tetraploid cross. Endosperm development in the reciprocal cross has phenotypic similarity to the tetraploid (seed parent)-diploid cross (Adams et al 2000). We are interested in understanding gene profiles and trends in expression underlying the endosperm development in the interploidy crosses as well as the fis and met1 mutant.
2010-01-09 | GSE19259 | GEO
Project description:Reciprocal crosses of a diploid Arabidopsis with different ploidies results in different endosperm development patterns and phenotype. Typically if the ploidy is higher on the maternal side, there are fewer endosperm cells which cellularize early, and conversely, if the paternal ploidy is higher, there is more number of endosperm cells which cellularize late. Crosses involving diploid and tetraploid Arabidopsis (C24) are viable, whereas crosses involving the diploid and hexaploid, even though exhibit the above mentioned directional trend in endosperm development, abort (Scott et al 1998). The 'maternalised' and 'paternalised' development of endosperm is also observed in crosses involving some Arabidopsis mutants. Mutants in the fis class of genes, e.g. fis1-medea, when crossed with a diploid Arabidopsis (pollen parent) show endosperm development-seed development similar to a diploid (seed parent) crossed with hexaploid pollen parent. Reciprocal crosses of homozygous met1 and diploid Arabidopsis also exhibit reciprocal trends in endosperm development, where a homozygous met1 mutant (seed parent) crossed with diploid is similar in phenotype to a diploid (seed parent) - tetraploid cross. Endosperm development in the reciprocal cross has phenotypic similarity to the tetraploid (seed parent)-diploid cross (Adams et al 2000). We are interested in understanding gene profiles and trends in expression underlying the endosperm development in the interploidy crosses as well as the fis and met1 mutant. 11 samples were used in this experiment.
2010-01-09 | E-GEOD-19259 | biostudies-arrayexpress
Project 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. Keywords: genotype comparison
2007-09-01 | GSE8278 | GEO
Project 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. Keywords: genotype comparison
2007-09-01 | GSE8275 | GEO
Project description:The goals of this study are to study the regulatory network of the two maize endosperm-specific transcription factors O2 and PBF by 16-DAP endosperm transcriptome profiling (RNA-seq) of their mutants and wild type. The results utilize the expression pattern of global genes regulated by PBF and O2 to elucidate their control for storage compounds synthesis in maize kernels.
2016-03-24 | GSE79513 | GEO
Project description:The goals of this study are to study the regulatory network of the two maize endosperm-specific transcription factors O2 and PBF by 16-DAP endosperm transcriptome profiling (RNA-seq) of their mutants and wild type. The results utilize the expression pattern of global genes regulated by PBF and O2 to elucidate their control for storage compounds synthesis in maize kernels. The 16-DAP endosperm transcriptome of wild type (WT) and mutants including opaque2, PbfRNAi and PbfRNAi;o2 were generated by RNA-seq with three biological replicates per genotype on Illumina HiSeqTM2500.
2016-03-24 | E-GEOD-79513 | biostudies-arrayexpress