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7 results for “Candidatus Liberibacter solanacearum”
Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis (Förster, 1848), Dyspersa pallida (Burckhardt, 1986), and Trioza urticae (Linnaeus, 1758) (Hemiptera: Psylloidea)
<p>Genomic datasets generated from three species of psyllid insect (Hemiptera: Psylloidea). This repository includes chromosome-scale genomic assemblies, mitochondrial genomes, co-assembled bacterial genomes, coding sequence annotations, transposable element annotations, and called SNPs, as well as files related to comparative genomics analyses. </p> <p><strong>Dataset contains:</strong><br><strong>From Trioza urticae genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - T. urticae derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From Dyspersa pallida (Trioza anthrisci) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. pallida mitochondrial genome assembly (fasta)<br> - D. pallida derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From Dyspersa apicalis (Trioza apicalis) genome assembly:</strong><br> - Genome assembly (fasta)<br> - Suspected contaminant seqeunces removed from the genome assembly (fasta)<br> - D. apicalis mitochondrial genome assembly (fasta)<br> - D. apicalis derived Candidatus Carsonella ruddii primary endosymbiont co-assembled genome (fasta)<br> - Transposable element annotations from EarlgreyTE:<br> - - Transpoable element library (fasta)<br> - - Predicted TEs (bed and gff)<br> - - Figures (pdf)<br> - Gene predictions from braker3+ :<br> - - Braker gene predictions (gft and aa) <br> - - Longest isoforms (faa)<br> - - - Interproscan annotation of gene predicitions (tsv)</p> <p><strong>From comparative genomics analysis:</strong><br> - Orthofinder analysis<br> - - Output of orthofinder analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (tsv and fasta)<br> - Cafe5 analysis<br> - - Output of cafe analysis comparing protein predictions from de novo psyllid assemblies with other hemiptera proteomes (excel, png, tab)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the Dyspersa taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. pallida taxonomic node (excel and tiff)<br> - - Enrichment analysis of GO and KO terms associated with expanded/contracted gene families at the D. apicalis taxonomic node (excel and tiff)<br> - - - Plots showing expansion/contraction of different orthogroups across the hemiptera phylogeny (png)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by iqtree2 (txt)<br> - Time calibrated phylogenetic tree of hemiptera including psyllids produced by astral (txt)<br> - C. Ca ruddii primary endosymbiont phylogenetic tree (txt)</p> <p><strong>From psyllid population resequencing:</strong><br> - Resequencing data<br> - - High confidence biallelic SNPs from D. pallida resequenced samples called against the de novo D. pallida genome assembly (vcf)<br> - - High confidence biallelic SNPs from D. apicalis resequenced samples called against the de novo D. apicalis genome assembly (vcf)<br> - - High confidence biallelic SNPs from resequenced samples called against the reference C. Ca ruddi endosymbiont genome assembly (vcf)<br> - - For suspected contanimant contigs removed from the D. pallida genome assembly; predicted identity, and coverage in each resequenced D. pallida sample (txt)<br> - - For suspected contanimant contigs removed from the D. apicalis genome assembly; predicted identity, and coverage in each resequenced D. apicalis sample (txt)<br> - - - Qualimap evaluation of resequencing data aligned to de novo psyllid genome for each resequenced sample (pdf)<br><br><br></p>
Transcriptome analysis of 'Candidatus Liberibacter solanacearum' in its psyllid vector, Bactericera cockerelli
GEO Series GSE57808. Candidatus Liberibacter solanacearum. 2 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis of 'Candidatus Liberibacter solanacearum' in its psyllid vector, Bactericera cockerelli [sexed insects]
GEO Series GSE81209. Candidatus Liberibacter solanacearum. 8 samples. Type: Expression profiling by high throughput sequencing.
Global gene expression analysis of two potato cultivars in response to “Candidatus Liberibacter solanacearum” infection
GEO Series GSE92312. Solanum tuberosum. 11 samples. Type: Expression profiling by high throughput sequencing.
Global gene regulation in tomato plant (Solanum lycopersicum) responding to vector (Bactericera cockerelli) feeding and pathogen (‘Candidatus Liberibacter solanacearum’) infection
GEO Series GSE95710. Solanum lycopersicum. 26 samples. Type: Expression profiling by high throughput sequencing.
Potato psyllids mount distinct gut responses upon infection with each of the two ‘Candidatus Liberibacter solanacearum’ haplotypes
GEO Series GSE206877. Bactericera cockerelli. 18 samples. Type: Expression profiling by high throughput sequencing.
Effects of ‘Candidatus Liberibacter solanacearum’ haplotypes A and B on tomato gene expression and geotropism
GEO Series GSE196951. Solanum lycopersicum. 12 samples. Type: Expression profiling by high throughput sequencing.
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