Transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. To test our hypothesis, we performed circRNA-Seq(RNase R treated) on B73 seedlings(third leaves of V3 stage), and uncovered 1,572 high-confidence maize circRNAs, which show distinct genomic features compared to linear transcripts. Comprehensive analyses showed that LINE1-like elements (LLE) and their reverse complementary pairs (RCPLLEs) are significantly enriched in the flanking regions of circRNAs.
Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize.
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Specimen part, Disease
View SamplesThis study is aimed to compare the gene expression between wild type and 35S:6MYC-HARP1 in response to wounding treatment.
No associated publication
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Age, Specimen part, Treatment
View SamplesThis study presented the differentially expressed genes post maize infected by Rhizoctonia solani.
No associated publication
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Specimen part
View SamplesIllumina/Solexa sequencing of CG3985 mutant and wildtype testes transcriptome (0-1 day males)
A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes.
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No sample metadata fields
View SamplesThe placenta has shown morphological and functional adaption in Meishan and Yorkshire pig breeds during late gestation. While the vast difference of uterine capacity and conceptus genotype between Western and Chinese pig breeds affects the pattern of placental development. Whether the placenta within Chinese pig breed also has similar adaptive changes is still unknown. So, we measured the weight and area of 80 Chinese indigenous Diannan small-ear pig placentas and further selected 6 placentas from extremely high and low litter size groups (HL and LL) for deep RNA-sequencing to detect the molecular basis relate to the observed placental phenotype difference.
No associated publication
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Sex, Specimen part
View SamplesCharacterization of circular RNAs in Ovarian cancer
No associated publication
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No sample metadata fields
View SamplesBph6 is a gene that confers rice high resistance to its devastating pest BPH. Understanding the molecular responses of the resistant and susceptible varieties would pave the way to controlling the pest more effectively.
No associated publication
Specimen part
View SamplesComparison of hippocampal gene expression between normal young animals and older animals with good spatial memory and older animals with poor spatial memory
No associated publication
No sample metadata fields
View SamplesThis SuperSeries is composed of the SubSeries listed below.
The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.
Age, Specimen part, Treatment
View SamplesBackground: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes the first genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation. Results: Genome-wide profiling revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified novel cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of primary versus redundant members of closely related gene families with respect to phosphate-starvation. Thus, among others, we show that PHO1 acts in shoot, whereas PHO1;H1 is likely the primary regulator in root. Conclusion: Our results uncover a much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the highest resolution of genome-wide data on plant nutrient stress to date.
The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.
Age, Specimen part, Treatment
View Samples