High-throughput approaches for profiling the 5'' ends of RNA degradation intermediates on a genome-wide scale are frequently applied in the validation of cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome beyond miRNA targets currently is largely unclear which limits the application of degradome. We provide multiple lines of evidence to show that ribosome footprints are widespread in the plant degradome. A 3-nt periodicity and a bias toward the translational frame were observed in the analysis of 5' truncated mRNA ends mapped to the coding sequence (CDS). In addition, predominant 5' termini of RNA degradation intermediates separated by a length equal to a ribosome-protected fragment were evident in the conserved peptide upstream open reading frames (uORFs). Through the analysis of degradome data, we uncovered novel ribosome stalling uORFs including a lineage specific uORF in the Brassicaceae family. Phased degradation signatures of stacked ribosomes were also identified in the CDS of multiple genes. Furthermore, we show that the binding of ARGONAUTE7 to a non-cleavable target site of miR390 might directly hinder ribosome movement. This work shows that the RNA degradome contains in vivo ribosome-protected mRNA fragments and demonstrates an alternative use of degradome data in the study of ribosome stalling.
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Specimen part
View SamplesThe regulation of transcriptome responses in zebrafish embryo exposure to triadimefon
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View SamplesIn order to gain a broad sampling of the Drosophila transcriptome, RNA-Seq experiments were performed at all stages of the Drosophila life cycle, and 12 independent cDNA libraries were generated, including embryonic, larval, pupal, and adult. Some libraries were staged as specific windows: 2-4 hour embryo, 14-16 hour embryo, 3rd instar larva, 3-day pupa, and 17-day adult. Additional libraries were derived from broadly staged mixed samples: embryo, larvae, and pupa. Three-day old male and female adults were sequenced separately for discovery of sex-specific variation. Finally, one library of mixed-age pupal RNA was sequenced in replicate as a validation of the technology. A total of 272 million paired-end reads of 64-75 base pairs in length were obtained, representing greater than 690x sequence coverage of the 30Mb Drosophila melanogaster transcriptome.
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View SamplesThis study is to investigate whether sepsis affected the differentiation program of HSPCs, we first used RNA-seq analysis to identify 12283 genes expression in HSCs sorted from control and septic mice.
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Sex, Specimen part, Disease
View SamplesOf 54,675 expressed sequence tags, microarray analysis revealed that 391 genes were differently expressed (>1.5-fold difference) between LA-PV junction and LAA, including genes related to arrhythmia, cell death, fibrosis, hypertrophy, and inflammation. Microarray and q-PCR produced parallel results in analyzing the expression of particular genes. The expression of paired like homeodomain-2 (PITX2) and its target protein (short stature homeobox-2 [SHOX2]) was greater in LA-PV junction than in LAA, which may contribute to arrhythmogenesis. Five genes related to thrombogenesis were up-regulated in LAA, which may implicate for the preferential thrombus formation in LAA. Genes related to fibrosis were highly expressed in LAA, which was reflected by intense ultrastructural changes in this region
Region-specific gene expression profiles in the left atria of patients with valvular atrial fibrillation.
Sex, Specimen part
View SamplesBackground: Atrial fibrillation (AF) causes atrial remodeling, and the left atrium (LA) is the favored substrate for maintaining AF. However, it remains unclear if AF remodels both atria differently and contributes to LA arrhythmogenesis and thrombogenesis.
Differential left-to-right atria gene expression ratio in human sinus rhythm and atrial fibrillation: Implications for arrhythmogenesis and thrombogenesis.
Sex, Age, Specimen part
View SamplesBackground: Heart failure (HF) causes various inflammatory responses. It remains unclear whether the inflammation the cause or effect of HF. Therefore, we wished to characterize the transcript profiles in the left ventricle (LV) of preserved and failed hearts respectively.
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Sex, Age, Specimen part
View SamplesBackground: In the remodeling process of the volume-overloaded heart, the extracellular matrix (ECM) may be dynamically modified to adapt to hemodynamic stress. We investigated the expression of ECM-related genes and modification of the elastin network in the remodeling process of the left ventricles (LVs) of rats with aortocaval fistulae. Methods and Findings: Gene array analysis identified 36 upregulated and 11 downregulated ECM-related genes during evolution from the compensated to the late decompensated phase. Ingenuity Pathway Analysis identified the formation of elastic fibers as an important biological function. Real-time PCR confirmed persistent upregulation of elastogenesis-associated genes, including elastin, lysyl oxidase, lysyl oxidase like-1, fibrillin 1, fibulin 2, versican and latent transforming growth factor beta binding protein 2 at various intervals. The expression levels and enzymatic activities of potent elastases, cathepsin S and cathepsin K increased during the early phase. Immunofluorescence confocal microscopy showed that the microstructure of the elastin network was preserved during the early phase, degraded during the compensated phase, partially repaired during the early decompensated phase, and reinforced during the late decompensated phase. Assessment of elastin concentrations in the LVs showed a consistent temporal pattern throughout the course.
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Sex, Specimen part
View SamplesBackground:To assess left ventricular (LV) transcriptome determinants of worsening LV function after mitral valve (MV) repair.
Ubiquitin Pathway Is Associated with Worsening Left Ventricle Function after Mitral Valve Repair: A Global Gene Expression Study.
Sex, Age, Specimen part
View SamplesBackground: The change of cellular energy metabolism in colorectal carcinogenesis is poorly understood. It is widely accepted tht most, if not all, colorectal cancers (CRCs) arise from adenomatous polyps (APs). Our aim was to characterize the mitochondrial and bioenergetic alternations in the adenoma-carcinoma sequence.
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Specimen part
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