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1,715 results for “Arabidopsis thaliana; Arabidopsis”
CSB3 transcriptome analysis (Arabidopsis thaliana)
GEO Series GSE35507. Arabidopsis thaliana. 2 samples. Type: Expression profiling by array.
Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana
GEO Series GSE35996. Arabidopsis thaliana. 8 samples. Type: Expression profiling by genome tiling array.
Global expression profiling to study the effect of sulfometuron methyl herbicide treatment on Arabidopsis thaliana
GEO Series GSE8912. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
Next Generation Sequencing of Wild Type (Col-0), fio1-1 and fio1-2 methylated RNA immunoprecipitation sequencing in Arabidopsis thaliana
GEO Series GSE171924. Arabidopsis thaliana. 3 samples. Type: Other.
Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time
GEO Series GSE190317. Arabidopsis thaliana. 34 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
ChIP-seq of histone modifications in Arabidopsis thaliana Col-0, clf-29, elf6-126,ino80-5 and elf6-126/ino80-5 using H2AZ, H3, H3K4me3 and H3K27me3 antibodies as well as input DNA control
GEO Series GSE283110. Arabidopsis thaliana. 44 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col and Ler reciprocal F1 hybrid embryo and endosperm
GEO Series GSE30511. Arabidopsis thaliana. 4 samples. Type: Expression profiling by high throughput sequencing.
Arabidopsis thaliana ecotype Col-0 versus T-DNA mutant sir1-1
GEO Series GSE20670. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
drn/drn-l expressing cells vs non-expressing cells-Embryonic patterning in Arabidopsis thaliana
GEO Series GSE19799. Arabidopsis thaliana. 10 samples. Type: Expression profiling by array.
The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution
GEO Series GSE173834. Arabidopsis thaliana. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
High-throughput sequencing of small RNAs from Arabidopsis thaliana
GEO Series GSE5228. Arabidopsis thaliana. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNAseq of Arabidopsis thaliana Col-0 inflorescences
GEO Series GSE74717. Arabidopsis thaliana. 2 samples. Type: Expression profiling by high throughput sequencing.
Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max
GEO Series GSE26199. Populus trichocarpa; Glycine max; Arabidopsis thaliana. 48 samples. Type: Expression profiling by array.
h3k27me3_c24-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
GEO Series GSE25058. Arabidopsis thaliana. 7 samples. Type: Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array.
An environment with strong gravitational and magnetic field alterations synergizes to promote variations in Arabidopsis thaliana callus global transcriptional state
Using diamagnetic levitation we have exposed A. thaliana in vitro callus cultures to five environments with different levels of effective gravity (from levitation i.e. simulated mg* to 2g*) and magnetic fields (10.1 to 16.5 Tesla) and we have compared the results with those of similar experiments done in a Random Position Machine (simulated micro g) and a Large Diameter Centrifuge (2g) free of high magnetic fields. Microarray analysis indicates that there are changes in overall gene expression of the cultured cells exposed to these unusual environments but also that gravitational and magnetic field produce synergic variations in the steady state of the transcriptional profile of A. thaliana. Significant changes in the expression of structural abiotic stress and secondary metabolism genes were observed into the magnet field. These results confirm that the strong magnetic field both at micro g* or 2g* has a significant effect on the expression of these genes but subtle gravitational effects are still observable. These subtle responses to microgravity environments are opposite to the ones observed in a hypergravity one. seven-condition experiment MM2D Arabidopsis culture callus control vs. Treatment (altered gravity simulation GBF). Three GBF were used (LDC (2g) + control RPM (mg) + control and Magnet (mg* 0.1g* 1g* 1.9g* 2g*) + control). Biological replicates: 3 replicates in all conditions and controls except 1.9g* (2 replicates)
Integrative Transcriptomics and Proteomics Profiling of Arabidopsis thaliana Elucidates Novel Mechanisms Underlying Spaceflight Adaptation
Spaceflight presents a unique environment with complex stressors, including microgravity and radiation, that can influence plant physiology at molecular levels. Combining transcriptomics and proteomics approaches, this research gives insights into the coordination of transcriptome and proteome in Arabidopsis’ molecular and physiological responses to Spaceflight environmental stress. Arabidopsis seedlings were germinated and grown in microgravity (µg) aboard the International Space Station (ISS) in NASA Biological Research in Canisters -Light Emitting Diode (BRIC LED) hardware, with the ground control established on Earth. At 10 days old, seedlings were frozen in RNA-later and returned to Earth. RNA-seq transcriptomics and TMT-labeled LC-MS/MS proteomic analysis of cellular fractionates from the plant tissues suggest the alteration of the photosynthetic machinery (PSII and PSI) in spaceflight, with the plant shifting photosystem core-regulatory proteins in an organ-specific manner to adapt to the microgravity environment. An overview of the ribosome, spliceosome, and proteasome activities in spaceflight revealed a significant abundance of transcripts and proteins involved in protease binding, nuclease activities, and mRNA binding in spaceflight, while those involved in tRNA binding, exoribonuclease activity, and RNA helicase activity were less abundant in spaceflight. CELLULOSE SYNTHASES (CESA1, CESA3, CESA5, CESA7) and CELLULOSE-LIKE PROTEINS (CSLE1, CSLG3), involved in cellulose deposition and TUBULIN COFACTOR B (TFCB) had reduced abundance in spaceflight. This contrasts with the increased expression of UDP-ARABINOPYRANOSE MUTASEs, involved in the biosynthesis of cell wall non-cellulosic polysaccharides, in spaceflight. Both transcripts and proteome suggested an altered polar auxin redistribution, lipid, and ionic intracellular transportation in spaceflight. Analyses also suggest an increased metabolic energy requirement for plants in Space than on Earth, hence, the activation of several shunt metabolic pathways. This study provides novel insights, based on integrated RNA and protein data, on how plants adapt to the spaceflight environment and it is a step further at achieving sustainable crop production in Space.
Approaches for Surveying Cosmic Radiation Damage in Large Populations of Arabidopsis thaliana Seeds- an Antarctic Example
The Cosmic Ray Exposure Sequencing Science (CRESS) payload system is a proof of concept experiment to assess the genomic impact of space radiation on seeds. CRESS was designed as a secondary payload for the December 2016 high-altitude high-latitude and long-duration balloon flight carrying the Boron And Carbon Cosmic Rays in the Upper Stratosphere (BACCUS) experimental hardware. Investigation of the biological effects of Galactic Cosmic Radiation (GCR) particularly those of ions with High-Z and Energy (HZE) is of interest due to the genomic damage this type of radiation inflicts. The biological effects of upper-stratospheric mixed radiation above Antarctica (ANT) were sampled using Arabidopsis thaliana seeds and were compared to those resulting from a controlled simulation of GCR at Brookhaven National Laboratory (BNL) and to laboratory control seed. The payload developed for Antarctica exposure was broadly designed to 1U CubeSat specifications (10cmx10cmx10cm <1.33kg) maintained 1 atm internal pressure and carried an internal cargo of four seed trays (about 580,000 seeds) and twelve CR-39 Solid-State Nuclear Track Detectors (SSNTDs). The irradiated seeds were recovered sterilized and grown on Petri plates for phenotypic screening. BNL and ANT M0 seeds showed significantly reduced germination rates and elevated somatic mutation rates when compared to non-irradiated controls with the BNL mutation rate also being significantly higher than that of ANT. Genomic DNA from mutants of interest was evaluated with whole-genome sequencing using PacBio SMRT technology. Sequence data revealed the presence of an array of genome structural variants in the genomes of M0 and M1 mutant plants.
Comparison of the spaceflight transcriptome of four commonly used Arabidopsis thaliana ecotypes
This experiment compared the spaceflight transcriptomes of four commonly used natural variants (ecotypes) of Arabidopsis thaliana using RNAseq. In nature, Arabidopsis is a native of Europe/Asia/Northwestern Africa and is found across the globe growing in a wide range of environments. The geographical spread of these various populations has led to a slow divergence leading to distinct ecotypes. Understanding the impact of this ecotypic variability is an important factor when using Arabidopsis as a model. Seeds of the ecotypes Col_0, Ler-2, Ws-2 and Cvi-0 were flown to the International Space Station as part of CRS-4 mission in the Biological Research in Canister (BRIC) hardware. The seeds were germinated on orbit, grown for 8 days and then fixed in RNAlater and frozen in the MELFI freezer for return to Earth. Once returned RNA was isolated and RNAseq performed to catalog the transcriptional patterns of the plants grown in space. An identical set of samples were grown in parallel on the ground to provide controls to allow assessment of transcriptional changes specifically associated with the spaceflight environment. This data release includes 48 out of 56 sample expression files with the remaining 8 files to be released at a later date.
Glycome profiling and immunohistochemistry uncover changes in cell walls of Arabidopsis thaliana roots during spaceflight: Advanced Plant EXperiment (APEX) 03-1 Raw Dataset
This study was conducted to uncover the underlying molecular mechanisms by which microgravity impacts cell wall architecture in the model plant Arabidopsis thaliana using the Vegetable Production System (Veggie) housed on the International Space Station (ISS). Based on our previous space flight studies using the Biological Research in Canisters (BRIC) hardware on the STS-131 Space Shuttle mission, we found that plants respond to microgravity in large part through the transcriptional reprogramming of genes that control cell wall remodeling. This follow-up spaceflight experiment called the Advanced Plant EXperiments (APEX 03-1) in Space was designed to use Veggie unit on the ISS and on the ground unit on the Space Station Processing Facility (SSPF) to probe deeper into spaceflight-induced cell wall associated transcript expression changes. In this study we used RNA-Seq in combination with glycome profiling (glycomics) to correlate spaceflight-induced gene expression changes with actual cell wall modifications within seedlings.
Transcriptomics analysis of etiolated Arabidopsis thaliana seedlings in response to microgravity
Gene expression profile of two-week-old etiolated Arabidopsis seedlings under microgravity on board space flight BRIC16 were compared with ground grown control in both wild-type and act2-3 mutant plants.
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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.