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38 results for “Xanthomonas oryzae; Xanthomonas oryzae pv. oryzae”
Genome assemblies of Xanthomonas oryzae pv. oryzae (PXO35, FXO38, Huang604) and Xanthomonas oryzae pv. oryzicola (BAI35, MAI23)
<p>Genome assemblies of <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> (<em>Xoo</em>) and <em>Xanthomonas oryzae</em> pv. <em>oryzicola</em> (<em>Xoc</em>). Genome assemblies of the <em>Xoo</em> strains PXO35, FXO38, Huang604 and the <em>Xoc</em> strains BAI35, MAI23, have been generated with Flye based on ONT reads. For each of these strains, we corrected the sequences encoding for transcription activator-like effectors (TALEs) with our TALE-correction pipeline (https://github.com/Jstacs/Jstacs/tree/master/projects/talecorrect). For Xoo PXO35, we additionally provide assemblies based on reads obtained from different sequencing methods (Illumina, PacBio, ONT) generated by a collection of (hybrid) assembly strategies and different polishing approaches applied to combinations of these.</p>
Data for: Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains
<p class="MsoNormal"><span>Bacterial leaf blight (BB) of rice, caused by <em>Xanthomonas oryzae </em>pv<em>. oryzae</em> (<em>Xoo</em>), threatens global food security and the livelihood of small-scale rice producers.<em> </em>Analyses of <em>Xoo</em> collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African <em>Xoo</em>, carry Asian-type TAL effectors targeting the sucrose transporter <em>SWEET11a</em> and iTALes suppressing <em>Xa1</em>. Phylogenomics clustered these strains with <em>Xoo</em> from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three <em>SWEET</em> promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of <em>Xoo</em>, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.</span></p>
Data for: Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains
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ProgressiveMauve alignment of Xanthomonas oryzae pv. oryzae PXO35 assembly variants
<p>Archive containing the alignment of eight assembly variants using different assembly programs and sequencing technologies. This alignment has been produced by the progressiveMauve algorithm (<a href="https://doi.org/10.1371/journal.pone.0011147">https://doi.org/10.1371/journal.pone.0011147</a>). The main alignment file is "PXO35_assembly_comparison", which can be opened and viewed interactively using the mauve program (<a href="https://darlinglab.org/mauve/download.html">https://darlinglab.org/mauve/download.html</a>).</p>
Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1
GEO Series GSE108504. Oryza sativa Japonica Group. 6 samples. Type: Expression profiling by high throughput sequencing.
Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice [datatset 2]
GEO Series GSE141995. Oryza sativa Japonica Group. 18 samples. Type: Non-coding RNA 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 GSE61607. Xanthomonas oryzae pv. oryzae KACC 10331. 14 samples. Type: Expression profiling by high throughput sequencing.
Xanthomonas oryzae pv. oryzae (Indian Isolate): Wild type vs. rpfF mutant
GEO Series GSE27809. Xanthomonas oryzae; Xanthomonas oryzae pv. oryzae. 4 samples. Type: Expression profiling by array.
Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice [datatset 1]
GEO Series GSE141775. Oryza sativa Japonica Group. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of in planta condition-dependent genes in Xanthomonas oryzae pv. oryzae KACC10331
GEO Series GSE89651. Xanthomonas oryzae pv. oryzae KACC 10331. 6 samples. Type: Expression profiling by high throughput sequencing.
Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv.oryzae constitutively expressing the X. oryzae pv. oryzicola TAL2a effector from the high cop
GEO Series GSE67958. Oryza sativa Japonica Group. 6 samples. Type: Expression profiling by high throughput sequencing.
Dynamic and coordinated expression changes of rice small RNAs in response to Xanthomonas oryzae pv. oryzae
GEO Series GSE58385. Oryza sativa Japonica Group. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Rice roots: Non-colonized (sterile) control vs. infected with Xanthomonas oryzae pv. oryzae strain PXO99 (Xan)
GEO Series GSE136706. Oryza sativa; Oryza sativa Japonica Group. 4 samples. Type: Expression profiling by array.
Dual RNA-seq of Xanthomonas oryzae pv. oryzicola infecting rice
GEO Series GSE126994. Oryza sativa; Xanthomonas oryzae pv. oryzicola. 5 samples. Type: Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Four genome assemblies of legacy Xanthomonas oryzae pv. oryzae isolated from Indian rice fields
<p>This dataset contains sequencing data for <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> strain M24, including Illumina reads (SRR30576374) and PacBio HiFi reads (SRR30576370) from a genome announcement titled, "Four genome assemblies of legacy <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> isolated from Indian rice fields."</p>
Transcriptome profile of rice genotypes IR24 and IRBB67 in interaction with Xanthomonas oryzae pv. oryzae under two temperature regimes
GEO Series GSE79011. Oryza sativa. 48 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola
GEO Series GSE9658. Xanthomonas oryzae pv. oryzae KACC 10331; Xanthomonas oryzae pv. oryzicola BLS256. 48 samples. Type: Expression profiling by array.
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.
Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice
GEO Series GSE141996. Oryza sativa Japonica Group. 20 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response
GEO Series GSE62488. Oryza sativa. 18 samples. Type: Expression profiling by high throughput sequencing.
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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.
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DANDI Archive for NWB datasets
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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.