Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1182739 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31249511_1.fastq.gz | Fastqsanger.gz | |||
| SRR31249511_2.fastq.gz | Fastqsanger.gz | |||
| SRR31249512_1.fastq.gz | Fastqsanger.gz | |||
| SRR31249512_2.fastq.gz | Fastqsanger.gz | |||
| SRR31249513_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Microarray hybridizations of a long-pod and a short-pod pool, each consisting of RNA from seven independent genotypes, were performed to reveal the gene regulatory basis underlying the genotypic pod length difference.
2017-04-30 | GSE80552 | GEO
Project description:Pod dehiscence is an important agronomic trait. Pod dehiscence would cause huge yield losses before soybean maturity. Although some of soybean pod dehiscence associated genes have been identified, the underlying mechanism of pod dehiscence is still not comprehensively explained. In this study, we have identified differentially expressed genes (DEGs) between shattering-resistant and shattering-susceptible soybean accessions based on transcriptome analyses of 10 soybean accessions. Long non-coding RNAs (lncRNAs) that may be involved in soybean pod dehiscence were also identified, and we constructed co-expression networks between mRNAs and lncRNAs. RNA sequencing results were further verified by real-time PCR. Furthermore, DEGs were screened through analyzing positions of soybean pod dehiscence quantitative trait locus (QTLs) and phenotypes of soybean pod dehiscence for achieving pod-dehiscence candidate genes.
2019-07-22 | GSE130010 | GEO
Project description:Postoperative delirium (POD) is a common postoperative complication in elderly patients. The exact mechanism of POD is still unclear. In order to reveal the effect of CircRNA on POD, We analyzed the differential expression profile of circRNAs by microarray technique in hippocampus of 12-month-old mice between tibial fracture and control group.
2021-12-16 | GSE190880 | GEO
Project description:Pod size varies among soybean cultivars, but the mechanism is largely unknown. We investigated pod size differences between two cultivars. The larger pod of ‘Tachinagaha’ was due to longer cell proliferation activity than in the shorter pod of ‘Iyodaizu’. Pod size of soybean 9 (GmPSS9), a member of the heat shock protein 70 family, was detected in a major QTL (qPSS on Chr. 2) as a candidate gene for determining pod length by QTL and expression QTL analysis. Expression of GmPSS9 in pods was higher in ‘Tachinagaha’ than in ‘Iyodaizu’ and was highest in early pod development. The difference in expression resulted from an indel polymorphism, Tachinagaha-specific-1, which has a 5′-UTR Py-rich stretch motif that boosts transcription. Treatment with an HSP70 inhibitor reduced plant height, pod length, and pod cell number. Our results identify GmPSS9 as a target gene for pod length which regulates cell number during early pod development.
2021-04-01 | GSE136772 | GEO
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:Quantitative analysis of the sequence determinants of transcription and translation regulation is of special relevance for systems and synthetic biology applications. Here, we developed a novel generic approach for the fast and efficient analysis of these determinants in vivo. ELM-seq (expression level monitoring by DNA methylation) uses Dam coupled to high-throughput sequencing) as a reporter that can be detected by DNA-seq. We used the genome-reduced bacterium Mycoplasma pneumoniae to show that it is a quantitative reporter. We showed that the methylase activity correlates with protein expression, does not affect cell viability, and has a large dynamic range (~10,000-fold). We applied ELM-seq to randomized libraries of promoters or 5’ untranslated regions. We found that transcription is greatly influenced by the bases around the +1 of the transcript and the Pribnow box, and we also identified several epistatic interactions (including the +1 and the “extended Pribnow”). Regarding translation initiation, we confirmed that the Shine-Dalgarno motif is not relevant, but instead, that RNA secondary structure is the main governing factor. With this in hand, we developed a predictor to help tailor gene expression in M. pneumoniae. The simple ELM-seq methodology will allow identifying and optimizing key sequence determinants for promoter strength and translation. The ELM-seq methodology allows both researchers and companies to identify and optimize in an easy and comprehensive manner, key sequence determinants for promoter strength and translation.
2017-08-29 | PXD005606 | Pride
Project description:Comparison of gene expression profiles of widespread peanut cultivars for exploring the expression data in pod and leaf with regard to signatures of artificial selection We investigated the overall expression by hybridizing the microarray (GPL13178) with RNA samples from pods and leaves of five selected representative peanut varieties (Fuhuasheng, Shitouqi, Yueyou116, Shanyou523, and Yueyou7), which were widely cultivated in different periods of the past fifty years in southern China. We used the RNA sample from Yueyou7 pod as a reference for all the pod hybridizations, and used the Yueyou7 leaf sample as a reference for all the leaf hybridizations. Field grown plants under normal irrigation were used for sample collection. Replicates with dye-swap were performed for each genotype.
2012-06-18 | E-GEOD-30128 | biostudies-arrayexpress
Project description:P. syringae pv. phaseolicola is the causal agent of the halo blight disease of beans (Phaseolus vulgaris L). The disease attacks both foliage and pods of plant host. Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. In this work we investigated the effect of bean pod extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without bean pod extract. Two RNA samples were compared, one prepared from cells grown in minimal medium M9 and the other from cells grown in minimal medium supplemented with bean pod extract.To control de biological variation that might interfere with data interpretation, a minimum of three biological replicates and two technical replicates (swap) were prepared.
2010-05-22 | E-GEOD-14625 | biostudies-arrayexpress
Project description:Limited studies on comparison of developmental (neuro)toxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl- (MtP), ethyl- (EtP) and propyl-paraben (PrP) in zebrafish embryos. Based on benchmark dose 5% (BMD5), embryonic mortality based-point of departure (M-PoD) values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0, M-PoD/50, M-PoD/10, and M-PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long-chained parabens were more toxic than short-chained parabens, as determined by M-PoD values of 154.1, 72.6, and 24.2 µM for MtP, EtP, and PrP, respectively. While exposure to EtP resulted in hyperactivity, no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP-exposed group are associated with the distinctly enriched pathways in signal, transport, calcium ion binding, and metal-binding. In contrast, exposure to MtP and PrP mainly disrupted the membrane and transmembrane, which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs, tentative transcriptomic-based PoD (T-PoD) values for each paraben were determined as MtP (2.68 µM), EtP (3.85 µM), and PrP (1.4 µM).
2023-08-07 | GSE239773 | GEO