Dosage effect on small RNA transcripts in maize copy number alterations
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Thomas Peterson
PROVIDER: E-GEOD-71959 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We sequenced 10 small RNA samples. 6 samples were taken from the 14-day old maize seedling tissue, and the other 4 samples were taken from 14-day old maize root tissue.
2015-09-04 | GSE71959 | GEO
Project description:We sequenced 9 mRNA samples taken from the 14-day old maize seedling tissue. These 9 samples are comprised by 3 genotypes and 3 replications. Examination of mRNA levels in each individual genotype.
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Project description:We sequenced 9 mRNA samples taken from the 14-day old maize seedling tissue. These 9 samples are comprised by 3 genotypes and 3 replications.
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Project description:Maize plants were grown under three different temperature regimes: 1) normal day / normal night; 2) hot day / normal night; 3) hot day / hot night. Kernels from developing ears were taken 14, 16, 18, 22, 26 and 40 days after pollination.
2015-02-19 | ST000290 | MetabolomicsWorkbench
Project description:Maize plants were grown under three different temperature regimes: 1) normal day / normal night; 2) hot day / normal night; 3) hot day / hot night. Kernels from developing ears were taken 14, 16, 18, 22, 26 and 40 days after pollination.
| ST000564 | MetabolomicsWorkbench
Project description:Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). Additionally, we profiled RNA pools (micro RNA (miRNA), siRNA and mRNA) using the same sequencing strategy. Keywords: Epigenetics, mRNA transcription and small RNAs H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings
2009-04-27 | E-GEOD-15286 | biostudies-arrayexpress
Project description: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. These reciprocal hybrids differ phenotypically from each other despite having identical nuclear genomes. Consistent with these phenotypic observations, 30-50% of genes were differentially expressed between these reciprocal hybrids. An eQTL experiment conducted to better understand the regulation of gene expression in inbred and hybrid lines detected ~4,000 eQTL associations. The majority of these eQTL act in trans to regulate expression of genes on other chromosomes. Surprisingly, many of the trans-eQTL, when heterozygous, differentially regulated transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. The design of the eQTL experiment controlled for cytoplasmic and maternal effects, suggesting that widespread paternal genomic imprinting contributes to the regulation of gene expression in maize hybrids. Keywords: eQTL, parent-of-origin GPL4521 - SAM1.2 (Reciprocal Hybrid Comparison): Six replications of B73xMo17 and Mo17xB73 were grown in growth chambers to tightly control environmental variation. Seeds from each genotype were taken from a single source (ear) for all six replications. Within each replication, genotypes were randomly assigned growth locations. Six healthy seedlings for each genotype and replication were harvested at two weeks of age. For each replication, B73xMo17 and Mo17xB73 were hybridized to the SAM1.2 microarray (GPL4521) using a randomized, alternate dye assignment. GPL3333 - SAM1.1 and GPL3538 - SAM3.0 (eQTL Experiment): Four biological replications of the RIL, B73xRIL, and Mo17xRIL cross-types were planted in growth chambers using seed from a single source for each genotype. Each RIL and its crosses onto B73 and Mo17 were planted using a split-plot design with RIL group (RIL and its cross onto B73 and Mo17) as the whole-plot treatment factor and cross-type (RIL, B73xRIL, and Mo17xRIL) as the split-plot treatment factor. The whole-plot portion of the experiment was designed as a randomized complete block design with four replications carried out on four separate occasions in the same environment. For the split-plot portion of the design, twelve seedlings of each RIL and its crosses were randomized within two adjacent flats in a growth chamber (six healthy seedlings per genotype were randomly chosen and pooled at harvest). For each replication, RIL, B73xRIL, and Mo17xRIL cross-types were hybridized to custom cDNA microarrays using a loop design such that each loop included all pairwise comparisons between the RIL and its crosses with B73 and Mo17. Four biological replications were hybridized to the SAM1.1 (GPL3333) array and two of the four biological replications were hybridized to SAM3.0 (GPL3538). RNA samples were alternately labeled to provide dye balance within each loop and replication. GPL8734 - Gene Expression between two maize reciprocal hybrids Heterosis refers to the enhanced agronomic performance of a hybrid relative to its (usually) inbred parents. We have previously documented widespread differences in gene expression in the B73xMo17 hybrid relative to its inbred parents B73 and Mo17 (Swanson, et al., 2006, PNAS). The reciprocal B73xMo17 and Mo17xB73 hybrids are both highly heterotic, but despite having identical nuclear genomes exhibit statistically significant differences in multiple traits. RNA-seq experiment was conducted to compare the gene expression globally between the two reciprocal hybrids. 1 samples from B73XMo17 and Mo17XB73 RNAs were extracted from a single replication of 14-day-old B73xMo17 and Mo17xB73 seedlings. RNAs were purified using DNaseI treatment followed by cleanup with the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) as per manufacturer instructions. Sequencing library construction was completed using the Illumina mRNA-Seq sample preparation kit. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.
2009-11-20 | E-GEOD-16136 | biostudies-arrayexpress
Project description:To identify miRNAs of Tribolium castaneum, one small RNA libraries for mix samples of eight development stage (including 1-day-old early embryo, 3-day-old late embryo, 1-day-old early larva, 20-day-old late larva, 1-day-old early pupa, 6-day-old late pupa, 1-day-old early adult, 7-day-old late adult) were constructed. Totally, 12,259,974 raw reads were obtained, 7,116,806 mappable reads were remained and 2,175,311 high-quality miRNA reads were identified after the small RNA digitalisation analysis. At last, 1,447 unique miRNAs which contained 274 conserved miRNAs, 245 known candidate miRNAs and 927 novel miRNAs were identified.
2016-10-20 | GSE81172 | GEO
Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both SAMs (SAMs per se plus P0 and P1) and above-ground portions of seedlings collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have 14,400 informative spots from maize. Statistical analyses showed that approximately 6.3% and 6.5% of the tested genes were significantly (p <0.0001) up- and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were also up-regulated (p <0.01). The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kinds of enzymes, suggesting these genes play important roles in meristem maintenance and the early stage of leaf development in maize. Interestingly, several retrotransposon-related genes were greatly up-regulated in the SAM. This finding raised the possibility that retrotransposons are involved in regulatory mechanisms of maize SAM. An experimental aim is to identify genes preferentially expressed in maize SAM by comparing the transcript abundant between SAMs and seedlings using cDNA microarrays that have 14,400 informative spots from maize.
2010-06-25 | E-GEOD-4722 | biostudies-arrayexpress
Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both whole SAMs (SAMs, P0 and P1) and whole seedlings (above ground part of seedlings) collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have about 30,000 maize cDNA clones. Statistical analyses showed that approximately 7% and 8% of the tested genes were significantly up-regulated and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were significantly up-regulated. Many histone genes and cell cycle related genes were also significantly up-regulated. Those observations validated our microarray results. The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kind of enzymes, suggesting those genes play important roles in meristem maintenance and the early stage of leaf development in maize. Surprisingly, several retrotransposon-related genes were greatly up-regulated with the statistical significance. This finding raised the possibility that retrotransposons are involved in regulatory mechanism of maize SAM. An experimental aim is to identify genes preferentially expressed in maize SAM by comparing the transcript abundant between whole SAMs and whole seedlings using cDNA microarrays that have about 30,000 maize cDNA clones.
2010-06-25 | E-GEOD-4004 | biostudies-arrayexpress