Ontology highlight
ABSTRACT:
PROVIDER: PRJNA561680 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10015225_1.fastq.gz | Fastqsanger.gz | |||
| SRR10015225_2.fastq.gz | Fastqsanger.gz | |||
| SRR10015226_1.fastq.gz | Fastqsanger.gz | |||
| SRR10015226_2.fastq.gz | Fastqsanger.gz | |||
| SRR10015227_1.fastq.gz | Fastqsanger.gz |
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Project description:cea06-01_uranyl_nitrate - time course uranyl nitrate response - Dynamic analyses of transcriptomic response to urany l nitrate - Plants are grown on sand and transfert in hydroponic culture during 2 days and then expose or not to 50uM uranyl nitrate at pH 4.5 in water or only to water at pH 4.5. Roots and leaves were collected independently after 2h, 6h and 30h of treament. Keywords: organ comparison,time course,treated vs untreated comparison
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Project description:Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of three well-established high throughput 3’-scRNAseq platforms: Drop-seq, 10x Chromium and BD Rhapsody; using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10x Chromium have similar but higher gene sensitivity than Drop-seq, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10x Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.
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Project description:cea06-01_uranyl_nitrate - time course uranyl nitrate response - Dynamic analyses of transcriptomic response to urany l nitrate - Plants are grown on sand and transfert in hydroponic culture during 2 days and then expose or not to 50uM uranyl nitrate at pH 4.5 in water or only to water at pH 4.5. Roots and leaves were collected independently after 2h, 6h and 30h of treament. Keywords: organ comparison,time course,treated vs untreated comparison 20 dye-swap - CATMA arrays
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Project description:Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. A. denitrificans strain BC can use chlorate, nitrate and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells a shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. Proteomic samples were prepared from Alicycliphilus denitrificans grown in the presence of different electron acceptors: chlorate, nitrate and oxygen. Proteins were separated by a short SDS gel and for each sample 4 in-gel digest slices were prepared. Peptide samples were measured by nLC LTQ-Orbitrap and the data were analysed with MaxQuant using default settings (1% FDR on peptide and protein level) and filtered extra to keep only proteins identified with at least 2 peptides and 1 unique and 1 unmodified peptide.
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Project description:The conversion of nitrate to ammonium, known as nitrate reduction, consumes large amounts of reductants in plants. Previous studies have observed that mitochondrial alternative oxidase (AOX) is upregulated under conditions of limited nitrate reduction, such as low or no nitrate availability, or when ammonium serves as the sole nitrogen (N) source. Electron transfer from ubiquinone to AOX bypasses the proton-pumping complexes III and IV, thereby consuming reductants efficiently. Therefore, the upregulation of AOX under conditions of limited nitrate reduction may help dissipate excessive reductants and mitigate oxidative stress. However, firm evidence supporting this hypothesis is lacking due to the absence of experimental systems capable of directly analyzing the relationship between nitrate reduction and AOX. To address this gap, we developed a novel culturing system that allows for the manipulation of nitrate reduction and AOX activities separately, without inducing N starvation, ammonium toxicity, or disrupting the nitrate signal. Using this system, we investigated genome-wide gene expression with RNA-seq to gain insight into the relationship between AOX and nitrate reduction.
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