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ShareScore release 0.9.0
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276 results for “plant transcriptomes”
Data from: Adaptation of a polyphagous herbivore to a novel host plant extensively shapes the transcriptome of herbivore and host
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Data from: The transcriptome response of Heliconius melpomene larvae to a novel host plant
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Data from: De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism
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Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species
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Data from: Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants
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Data from: De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana
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Data from: Comparative transcriptome resources of eleven Primulina species, a group of “stone plants” from a biodiversity hotspot
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Data from: The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes
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Data from: A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes
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The Arabidopsis spaceflight transcriptome: a comparison of whole plants to discrete root hypocotyl and shoot responses to the orbital environment
Arabidopsis thaliana was evaluated for its response to the spaceflight environment in three replicated experiments on the International Space Station. Two approaches were used; GFP reporter genes were used to collect gene expression data in real time within unique GFP imaging hardware and plants were harvested on orbit to RNAlater for subsequent analyses of gene expression with using Affymetrix and SAGE transcriptome analyses. Three tissue types were examined (leaves hypocotyls and roots) and compared to analyses conducted with whole plants. Transcriptome analyses with whole plants suggested that the spaceflight environment had little impact on the transcriptome of arabidopsis however closer examination of selected tissues revealed that there are a number of tissue-specific responses that arabidopsis employs to respond to this novel environment
RNA-Seq transcriptome analysis of reactive oxygen species gene network in Mizuna plants grown in long-term space flight
Space environment is suspected to generate reactive oxygen species (ROS) and induce oxidative stress in plants however little is known about the gene expression of ROS gene network in plants grown in long-term space flight. RNA-Seq was used to define the large-scale gene expression profiles of Mizuna harvested after 27 days cultivation in the international space station to understand the molecular response and adaptation to space environment.Results: Total reads of transcripts from the Mizuna grown in the international space station as well as on the ground by RNA-Seq using next generation sequencing technology showed 8,258 and 14,170 transcripts up- and down-regulated in the space-grown Mizuna respectively when compared with those from the ground-grown Mizuna. A total of 20 in 32 ROS oxidative marker genes were up-regulated including high expression of 4 hallmarks and preferentially expressed gene associated with ROS-scavenging genes was thioredoxin glutaredoxin and alternative oxidase genes. In the transcription factors of ROS gene network MEKK1-MKK4-MPK3 OXI1-MKK4-MPK3 and OXI1-MPK3 of MAP cascades induction of WRKY22 by MEKK1-MKK4-MPK3 cascade induction of WRKY25 and repression of ZAT7 by Zat12 were suggested. RbohD and RbohF genes were up-regulated preferentially in NADPH oxidase genes which produce ROS.Conclusions: Our large-scale transcriptome analysis demonstrated that the space environment induced oxidative stress and ROS gene network was activated in the space-grown Mizuna some of which were common genes up-regulated by abiotic and biotic stress and were preferentially up-regulated genes by the space environment even though Mizuna grew in the space as well as on the ground showing that plants could acclimate to the space environment by reprograming the expression of ROS gene network.
Genetic Dissection of the Spaceflight Transcriptome Responses in Plants: are some responses unnecessary?
Experimentation on the International Space Station has reached the stage where repeated and nuanced transcriptome studies are beginning to illuminate the structural and metabolic differences between plants grown in space compared to plants on the Earth. Genes that are important in setting up the spaceflight responses are being identified; their role in spaceflight physiological adaptation are increasingly understood and the fact that different genotypes adapt differently is recognized. However the basic question of whether these spaceflight responses are required for survival has yet to be posed and the fundamental notion that spaceflight responses may be non-adaptive has yet to be explored. Therefore the experiments presented here were designed to ask if portions of the plant spaceflight response can be genetically removed without causing loss of spaceflight survival and without causing increased stress responses. The CARA experiment compared the spaceflight transcriptome responses of two Arabidopsis ecotypes Col-0 and WS as well as that of a PhyD mutant of Col-0. When grown with the ambient light of the ISS phyD displayed a significantly reduced spaceflight transcriptome response compared to Col-0 suggesting that altering the activity of a single gene can actually improve spaceflight adaptation by reducing the transcriptome cost of physiological adaptation. The WS genotype showed an even simpler spaceflight transcriptome response in the ambient light of the ISS more broadly indicating that the plant genotype can be manipulated to reduce the transcriptome cost of plant physiological adaptation to spaceflight and suggesting that genetic manipulation might further reduce or perhaps eliminate the metabolic cost of spaceflight adaptation. When plants were germinated and then left in the dark on the ISS the WS genotype actually mounted a larger transcriptome response than Col-0 suggesting that the in-space light environment affects physiological adaptation which further implies that manipulating the local habitat can also substantially impact the metabolic cost of spaceflight adaptation.
Host plant adaptation of a polyphagous herbivore shapes transcriptome of both herbivore and host
GEO Series GSE68708. Tetranychus urticae. 12 samples. Type: Expression profiling by array.
Transcriptomic analysis of the tomato plant response to Tuta absoluta herbivory
GEO Series GSE200795. Solanum lycopersicum. 12 samples. Type: Expression profiling by high throughput sequencing.
From transcriptomics to phenomics to reveal adaptation response of Lactobacillus plantarum C2 in plant substrates
GEO Series GSE68188. Lactiplantibacillus plantarum. 8 samples. Type: Expression profiling by array.
Alternative Developmental and Transcriptomic Responses to Host Plant Water Stress in a Butterfly metapopulation
GEO Series GSE159376. Melitaea cinxia. 78 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis Arabidopsis Col-0 plants grown in presence of SynComCol-0, SynCommfec and under axenic condition in Gnotopot growth system
GEO Series GSE218962. Arabidopsis thaliana. 9 samples. Type: Expression profiling by high throughput sequencing.
Temporal comparison of leaf transcriptomes between early-flowering Arabidopsis thaliana atx1/atx3/atx4 triple mutants and vegetative WT Col-0 plants of the same age.
GEO Series GSE134177. Arabidopsis thaliana. 36 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis indicates the involvement of herbicide-responsive and plant-pathogen interaction pathways in the development of resistance to ACCase inhibitors in Apera spica-venti
GEO Series GSE204788. Apera spica-venti. 2 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome of anthers from both the ZmCCT-active and non-transgenic control plants.
GEO Series GSE188462. Zea mays. 18 samples. Type: Expression profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.