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229
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ShareScore release 0.7.1
Dataset results
229 results for “plant genomics”
Metagenome-assembled genomes from two genera of pitcher plants and three freshwater lakes
<p>Illumina shotgun metagenome sequences from <em>Sarracenia </em>and <em>Nepenthes </em>pitcher plants (originally published in Bittleston et al. 2018, MG-RAST RRID: SCR_004814; mgp15454) and three freshwater lakes (Consensus Lake, New York, USA (SRR15064816), Lake Mendota, Wisconsin, USA (SRR11647637), and Lake Samiti, Sikkim, India (SRR10757258)) were binned using CONCOCT v1.1.0 (Alneberg et al. 2014). Bins were further refined using anvi’o’s interactive interface v7.1 (Eren et al. 2015).</p>
Data from: Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon
In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes.
Genomics-based annotations help unveil the molecular composition of edible plants
<p>Supporting Data for https://doi.org/10.1101/2022.01.24.477528.</p> <p><a href="https://zenodo.org/api/files/cec6e8af-1eca-40ae-bd81-c9a8ff9a67aa/kinetics_all_Plants_df_fb_avg.csv">kinetics_all_Plants_df_fb_avg.csv</a> - A table summarizing the thermodynamic feasibility approach results including the score, is it found in the experiments, first block inchIKey, the group of full inchIKeys for that first block representation, compound mass and the number of reactions the compound is in.</p> <p><a href="https://zenodo.org/api/files/cec6e8af-1eca-40ae-bd81-c9a8ff9a67aa/Metabolon_Data_known.xlsx">Metabolon_Data_known.xlsx</a> - a spreadsheet containing the metabolomics experiment results for edible plants tested.</p> <p><a href="https://zenodo.org/api/files/cec6e8af-1eca-40ae-bd81-c9a8ff9a67aa/plant_masterTable_100621.csv">plant_masterTable_100621.csv</a> - a CSV file containing the list of compounds' InchIKeys used in this work and their annotation association. One denotes annotation association to the data source in a given column.</p> <p>table_s2.csv - a CSV file describing the comparison of the data used in this work to CoconutDB, a plant natural product database.</p>
Bioactive Plant Foods: Effects on Functional Bioavailability and Genomic Stability
ClinicalTrials.gov study NCT00963118. IPD Sharing: Not stated. Countries: 1. Publications: 0.
N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [RNA-Seq Nipponbare]
GEO Series GSE108782. Oryza sativa. 2 samples. Type: Expression profiling by high throughput sequencing.
Landscape genomics analysis: A comprehensive guide to enhance the conservation and use of plant genetic resources
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Data from: A genome for gnetophytes and early evolution of seed plants
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Data from: The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)
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Data from: Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species
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Data from: Genome assembly and annotation of the medicinal plant Calotropis gigantea, a producer of anticancer and antimalarial cardenolides
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Data from: Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon
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The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [ChIP-Seq]
GEO Series GSE288765. Lemna minor; Lemna japonica; Lemna turionifera. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The plant POLYMERASE ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome-wide [RNA-seq]
GEO Series GSE244848. Arabidopsis thaliana. 9 samples. Type: Expression profiling by high throughput sequencing.
Time-resolved genome-wide pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) via RNA-Seq
GEO Series GSE154542. Xanthomonas oryzae pv. oryzae. 6 samples. Type: Expression profiling by high throughput sequencing.
Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen
GEO Series GSE233220. Eucalyptus grandis; Armillaria luteobubalina. 28 samples. Type: Expression profiling by high throughput sequencing.
A genome-scale analysis of mitochondrial-associated mRNAs in plants: upstream AUGs in 5’UTRs alter mRNA targeting
GEO Series GSE91388. Solanum tuberosum. 6 samples. Type: Expression profiling by high throughput sequencing.
Genome wide expression analysis of psaA and psbA tobacco mutant plants.
GEO Series GSE23626. Solanum lycopersicum; Nicotiana tabacum. 6 samples. Type: Expression profiling by array.
The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [smallRNA-Seq]
GEO Series GSE238134. Lemna japonica; Lemna gibba; Wolffia australiana; Spirodela polyrhiza. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [ChIP-Seq]
GEO Series GSE128168. Arabidopsis thaliana. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction [Hi-C]
GEO Series GSE238132. Lemna turionifera; Lemna gibba; Lemna japonica; Lemna minor; Wolffia australiana. 5 samples. Type: Other.
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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.