Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
62
datasets available to search
ShareScore release 0.9.0
Dataset results
62 results for “Neisseria gonorrhoeae”
REPIN population analysis in 130 Neisseria meningitidis and N. gonorrhoeae genomes
<p>This dataset is the output of RAREFAN (http://rarefan.evolbio.mpg.de/) a webserver to identify REPIN populations across an entire bacterial species. The data was created using the following command "java -jar -Xmx10g rarefan.jar neisseria/in/ neisseria/out/ Nmen_2594.fas 55 21 neisseria/in/NMAA_0235.faa neisseria.nwk 1e-80 true 1"</p> <p>All input files are located in the folder neisseria/in/, all output data is located in neisseria/out/.</p> <p>The input files include the 130 fasta formatted <em>Neisseria</em> genome files (*.fas) and a RAYT protein sequence called NMAA_0235.faa.</p> <p>The output files include the following:</p> <p>A phylogenetic tree "neisseria.nwk" of all genomes generated with andi (<a href="http://github.com/evolbioinf/andi/">http://github.com/evolbioinf/andi/</a>) and clustDist (http://guanine.evolbio.mpg.de/problemsBook/node1.html).</p> <p>A file containing the frequencies of all 21bp long sequences found in the Nmen_2594 genome: Nmen_2594.wfr</p> <p>A file containing all 21bp long sequences that occur more frequently than 55 times in the Nmen_2594 genome: Nmen_2594.overrep</p> <p>A file containing information on the RAYTs and their cooccurrence with different REPIN populations: prox.stats</p> <p>A file containing the nucleotide sequences of all NMAA_0235.faa relatives identified with BLAST+ in the <em>Neisseria </em>species: yafM_relatives.fna</p> <p>maxREPIN_[0-5] Contains the most frequent REPIN identified for each sequence type in each <em>Neisseria</em> strain.</p> <p> presAbs_[0-5].txt Contains for each strain information on the number of RAYTs, the number of REPINs, the master sequence, the number of master sequences, the entire REP/REPIN population size, the number of REPIN clusters that contain more than 10 sequences, all REPINs in the population as well as all REPINs that differ to the master sequences in at most three nucleotides.</p> <p>rayt_[strain name].tab contains location information for each identified RAYT relative for each strain. The files can be viewed with artemis.</p> <p>results.txt contains for each strain the frequency of the six identified 21bp long seeds.</p> <p>There is one folder called groupSeedSequences, which includes the data for identifying the most common 21 bp long sequences in <em>Neisseria meningitidis</em> WUE 2594. All 21bp long sequences in the genome that occur more frequently than 55 times are sorted into 6 sequence groups. These sequence groups are stored in the files Group_Nmen_2594_*.out and .out.fas. There is also a Nmen_2594_words.tab file, which contains the locations of all overrepresented 21bp long sequences in the Nmen_2594 genome. This file can be viewed in artemis (https://www.sanger.ac.uk/tool/artemis/) together with the Nmen_2594 genome file. The most common sequence in each group is used as a seed sequence to determine REPIN populations across all 130 genomes.</p> <p> </p> <p>For each genome there are six output folders (ending in _0 to _5), for each sequence group one.</p> <p>Each folder contains the following files:</p> <p>*.dd: Degree distribution of the REPIN network, where each REPIN is a node. A REPIN is connected to another REPIN if they differ in exactly one position. The degree distribution is a histogram of the number of connections of all the nodes. </p> <p>*.hist For the largest sequence cluster determined by mcl that consists of REPINs (two REPs in inverted orientation) this file contains the number of REPINs in each sequence class. Sequence class 0 is the master sequence. By definition the most common REPIN in the sequence population. Sequence class 1 contains all REPINs differing in exactly one position to the master sequence. Sequence class 2 contains REPINs differing in 2 positions etc.</p> <p>*.mcl Contains the clustering output by mcl. Each line contains the member of a cluster. Lines are sorted by cluster size.</p> <p>*.mw Contains the most common 21bp long sequence and its frequency in the genome, which is the basis for identifying first all related REP sequences and from those the REPINs formed by these REP sequences.</p> <p>*.nodes The identity and frequency of all REPINs and REP sequences for either all sequences or only for the largest sequence cluster.</p> <p>*.ss Contains REPINs and REP sequences as well as their positions in fasta format. Position information starts with the location in genome fasta file (first sequence is 0...) followed by the start and end position of the entire REPIN/REP sequence. </p> <p>*.ss.REP REP sequence information in fasta format.</p> <p>*.tab Location in tab format. Can be used to display locations of REPs and REPINs in the genome via artemis.</p> <p>*_[0-9].ss Contains REPIN/REP sequence information for each subcluster separately.</p> <p>*_[0-9].tab Contains the location of REP/REPINs for each subcluster separately for viewing in artemis.</p> <p>*allSeed.nw Contains network connections between nodes of all sequences. Can be used to view network in for example R or cytoscape together with the nodes file.</p> <p>*largestCluster.nodes Information on nodes only from the largest REPIN cluster.</p> <p>*largestCluster.ss *.ss file for the largest REPIN cluster.</p> <p>*largestCluster.tab *.tab file for the largest REPIN cluster.</p> <p>*_rayt_repin_prox.txt shows which REPIN/REP cluster is in proximity to any of the RAYT genes identified in the genome (within 200bp).</p> <p>And a subfolder that contains the complete sequences (including the variable region) for all identified REPs and REPINs.</p> <p>The dataset was generated using the following external tools:</p> <p>andi for tree building:</p> <p>B Haubold, F Klötzl, and P Pfaffelhuber. <strong>andi: fast and accurate estimation of evolutionary distances between closely related genomes.</strong> Bioinformatics, 2015 vol. 31 (8) pp. 1169-1175.</p> <p>MCL for REPIN population clustering:</p> <p>A J Enright, S Van Dongen, and C A Ouzounis. <strong>An efficient algorithm for large-scale detection of protein families.</strong> Nucleic Acids Research, 2002 vol. 30 (7) pp. 1575-1584.</p> <p>BLAST+ for identifying RAYT relatives in the different genomes:</p> <p>C Camacho, G Coulouris, V Avagyan, N Ma, J Papadopoulos, K Bealer, and T L Madden. <strong>BLAST+: architecture and applications.</strong> BMC Bioinformatics, 2009 vol. 10 (1) pp. 421-9.</p>
Dataset for Antimicrobial resistance of Neisseria gonorrhoeae in Germany: low levels of cephalosporin resistance but rising azithromycin resistance
<p>This is Dataset used for Publication "Antimicrobial resistance of <em>Neisseria gonorrhoeae</em> in Germany: low levels of cephalosporin resistance but rising azithromycin resistance" and contains data on Information on performed Neisseria gonorrhoeae AMR tests in sentinel Laboratories as well as AMR testing in consiliary Laboratory.</p>
Comparing mail-in self-collected specimens sent via United States Postal Service versus clinic-collected specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in extra-genital sites data set
<p>This data set was used to evaluate the concordance between clinic-collected extra-genital specimens and self-collected mailed-in extra-genital specimens among participants seeking sexually transmitted infection testing at a free clinic in Hollywood, CA. The newest version of the file reflects sample adequacy control (SAC) cycle threshold values for each participant.</p>
Evaluation of EVO100 for Prevention of Urogenital Chlamydia Trachomatis and Neisseria Gonorrhoeae Infection
ClinicalTrials.gov study NCT04553068. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Efficacy of Immunization With 4C-MenB in Preventing Experimental Urethral Infection With Neisseria Gonorrhoeae
ClinicalTrials.gov study NCT05294588. IPD Sharing: YES. Countries: 1. Publications: 1.
Clinical Validation of a Molecular Test for Ciprofloxacin-Susceptibility in Neisseria Gonorrhoeae
ClinicalTrials.gov study NCT02961751. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Use of Abbott RealTime CT/NG to Detect Chlamydia Trachomatis [CT] & Neisseria Gonorrhoeae [NG] in Men Who Have Sex With Men [MSM]
ClinicalTrials.gov study NCT01291264. IPD Sharing: Not stated. Countries: 1. Publications: 11.
Experimental Human Infection With Neisseria Gonorrhoeae
ClinicalTrials.gov study NCT03840811. IPD Sharing: Not stated. Countries: 1. Publications: 2.
A Dose-Ranging Study Evaluating the Efficacy, Safety, and Tolerability of GSK2140944 in the Treatment of Uncomplicated Urogenital Gonorrhea Caused by Neisseria Gonorrhoeae
ClinicalTrials.gov study NCT02294682. IPD Sharing: Not stated. Countries: 3. Publications: 3.
Antenatal Chlamydia Trachomatis and Neisseria Gonorrhoeae Testing to Prevent Adverse Neonatal Consequences
ClinicalTrials.gov study NCT04955717. IPD Sharing: NO. Countries: 2. Publications: 2.
Neisseria gonorrhoeae clustering to reveal major European WGS-based genogroups in association with antimicrobial resistance (cgMLST and MScgMLST schemas, allelic profile matrices and GrapeTree input file)
<p>This dataset refers to the gene-by-gene analysis of 3791 <em>Neisseria gonorrhoeae</em> genomes from 21 European countries and includes the used cgMLST and MScgMLST loci schemas prepared for the chewBBACA core suite, as well as the associated allelic profile matrices for all genomes. Additionally a <em>.json</em> file is made available for direct input in the GrapTree vizualization software for data/metadata exploration. </p> <p>All novel raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB36482). Additional raw sequence read data used were retrieved from the following ENA BioProjects: PRJEB14933; PRJEB2124; PRJEB23008; PRJEB26560; PRJEB9227; PRJNA275092; PRJNA348107; PRJNA473385; PRJNA315363. </p>
Neisseria gonorrhoeae IMRS Data
Open the record for dataset details and reuse information.
Dataset for External quality assessment (EQA) of Neisseria gonorrhoeae antimicrobial susceptibility testing in primary laboratories in Germany
<p>This dataset is used for the publication "External quality assessment (EQA) of Neisseria gonorrhoeae antimicrobial susceptibility testing in primary laboratories in Germany" and contains data on performed Neisseria gonorrhoeae AMR tests in sentinel Laboratories.</p>
The Pharmacokinetics of Extended Duration High-dose Cefixime for the Decreased Susceptibility of Neisseria Gonorrhoeae: A Phase I Pilot Study
ClinicalTrials.gov study NCT01949363. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Comparison of Efficacy of Two Combination Regimens for the Neisseria Gonorrhoeae and Chlamydia Coinfection
ClinicalTrials.gov study NCT05216744. IPD Sharing: NO. Countries: 1. Publications: 1.
Detection of Chlamydia Trachomatis, Neisseria Gonorrhoeae and Mycoplasma Genitalium by Real-time Multiplex Polymerase Chain Reaction (PCR) After Pooling Pharyngeal, Anorectal and Urinary Samples
ClinicalTrials.gov study NCT03568695. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Data from: Evolution of the exclusively human-pathogen Neisseria gonorrhoeae: human-specific engagement of immunoregulatory Siglecs
Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhea exclusively in humans and uses multiple strategies to infect, including acquisition of host sialic acids that cap and mask lipooligosaccharide termini, while restricting complement activation. We hypothesized that gonococci selectively target human anti-inflammatory sialic acid-recognizing Siglec receptors on innate immune cells to blunt host responses, and that pro-inflammatory Siglecs and SIGLEC pseudogene polymorphisms represent host evolutionary adaptions to counteract this interaction. N. gonorrhoeae can indeed engage multiple human but not chimpanzee CD33rSiglecs expressed on innate immune cells and in the genitourinary tract––including Siglec-11 (inhibitory) and Siglec-16 (activating), which we detected for the first time on human cervical epithelium. Surprisingly, in addition to LOS-sialic acid, we found that gonococcal porin (PorB) mediated binding to multiple Siglecs. PorB also bound preferentially to human Siglecs and not chimpanzee orthologs, modulating host immune reactions in a human-specific manner. Lastly, we studied the distribution of null SIGLEC polymorphisms in a Namibian cohort with a high prevalence of gonorrhea, and found that uninfected women preferentially harbor functional SIGLEC16 alleles encoding an activating immune receptor. These results contribute to the understanding of the human specificity of N. gonorrhoeae and how it evolved to evade the human immune defense.
Clinical Study of a Single-Use, Point-of-Care Molecular Diagnostic Device for the Detection of Neisseria Gonorrhoeae (NG), Trichomonas Vaginalis (TV), and Chlamydia Trachomatis (CT) Utilizing Vaginal
ClinicalTrials.gov study NCT03596151. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Safety and Efficacy of GSK Neisseria Gonorrhoeae GMMA (NgG) Investigational Vaccine When Administered to Healthy Adults 18 to 50 Years of Age.
ClinicalTrials.gov study NCT05630859. IPD Sharing: YES. Countries: 8. Publications: 0.
Mucosal Immunity Against Neisseria Gonorrhoeae After 4CMenB Vaccination
ClinicalTrials.gov study NCT04722003. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
Understand access before you commit
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.