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.
278
datasets available to search
ShareScore release 0.9.0
Dataset results
278 results for “oligonucleotides”
Oligonucleotide probes used for comparative mapping in lupin species
<p>The supplementary list of oligonucleotide probes generated in Chorus software. Filtered probes were used in oligo-FISH comparative mapping of lupin species. Detailed description provided in the article: 'The puzzling fate of a lupin chromosome revealed by reciprocal oligo-FISH and BAC-FISH mapping'.</p>
Whole-genome capture and sequencing of Mycobacterium tuberculosis directly from clinical samples - Design of RNA oligonucleotide baits for Agilent Technologies' SureSelect target enrichment
<p>This dataset comprises the sequence of <strong>44 278 RNA oligonucleotide "baits" (120 bp each) </strong>designed to perform <strong>whole-genome capture and sequencing of <em>Mycobacterium tuberculosis</em> directly from clinical samples</strong> (DNA) using Agilent Technologies’ SureSelect target enrichment system following the Illumina paired-end multiplexed sequencing library protocol. </p> <p>RNA oligonucleotide “baits” were designed to span the ∼4.5 Mb of the <em>M. tuberculosis</em> genome. In brief, the reference genome sequence of the MTBC H37Rv strain (Genbank #AL123456) was <em>in silico</em> fragmented into 120 bp sequences twice, to ensure an overlap of 60 bp between sequences. Due to their rich GC content, which could interfere with DNA capture, all MTBC genes of the PE, PPE and PE-PGRS family were also independently fragmented into 120 bp sequences, in order to increase capture sensitivity. All resulting sequences were BLASTn searched against the Human Genomic + Transcript database to excluded homologous sequences to the human genome. Overall, a total of 42,278 RNA probes were generated and this custom bait library was then uploaded to the SureDesign software (https://earray.chem.agilent.com/suredesign) and synthesized by Agilent Technologies. During synthesis, the 2198 sequences complementary to the PE, PPE and PE-PGRS family were unbalanced 8:1 to potentiate capture.</p> <p>More details can be found in the following publication:</p> <p>- Macedo, R., Isidro, J., Ferreira, R., Pinto, M., Borges, V., Duarte, S., Vieira, L., & Gomes, J. P. (2023). Molecular Capture of <em>Mycobacterium tuberculosis</em> Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. <em>International journal of molecular sciences</em>, <em>24</em>(3), 2912. https://doi.org/10.3390/ijms24032912</p>
DNA-HDXMS_XchangeDB: A dataset of Hydrogen-Deuterium eXchange native Mass Spectrometry experiments on DNA oligonucleotides
<p>The DNA-HDXMS_XchangeDB dataset contains HDX/native MS exchange kinetics and metadata of a reference set of DNA oligonucleotides.</p> <p> </p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Comparison of mono-, MiL- and CARD-FISH on LR-White embedded <em>Olavius algarvensis</em> cross sections A: Ethanol preserved specimen, cu = cuticle, sym = symbionts, sep = septum, epi = epidermis, mu = muscle, vbv = ventral blood vessel & nerve chord, chl = chloragogen tissue, grid square = example of region shown in images B, C, D and E.</p> <p>Probes for Gammaproteobacteria (Gam42a; green) and a subgroup of sulfate-reducing Deltaproteobacteria (DSS658; red) on B) mono-FISH on ethanol preserved specimen, 19 hour hybridisation. C) mono-FISH on ethanol preserved specimen, 3 hour hybridisation and D) CARD-FISH on Carnoy’s / PFA fixed specimen, 3-hour hybridisation. E) MiL-FISH on Carnoy’s / PFA fixed specimen, 3 hour hybridisation. Scale bar = 5 µm.</p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Sections of LR-White embedded <em>Olavius algarvensis </em>eggs. A) DAPI stained overview of egg after first cleavage, grid square = region in B, cle = cleavage. B) Gamma- (ii) and Delta- (i) proteobacteria hybridised with 4x labelled Gam42a & 4x labelled DSS658 probe respectively. Autofluorescence of egg yolk is overcome and bacteria are seen to closely associated with the developing embryo. y = egg yolk C) DAPI stained overview of juvenile worm in egg, grid square = region in D. D) Gamma 1 symbiont phylotype (iii) hybridised with 16S rRNA specific probe labelled with 2x FITC and 2x Cy3 to produce yellow in the overlay. Symbiont cells are incorporated between cuticle and epidermis and in close proximity to egg yolk. y = egg yolk, c = cuticle. Scale: A & C = 50 µm, B & D = 5 µm.</p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Epifluorescence images of MiL-FISH labelled microorganisms: A) <em>Beggiatoa sp. </em>hybridised with Gam42a, B) <em>Desulfococcus biacutus </em>with DSS658, C) <em>Roseobacter sp. </em>with Ros537, D) <em>Sulfurimonas denitrificans </em>with EPSY914, E) <em>Rhodopirellula sp. </em>SH1 T with PLA46, F) <em>Gramella forsetii </em>with CF319a, G) <em>Metallosphaera sedula </em>with Arch915, H) Composite image of all seven microbial partners in an artificial mix. Letters correlate to images of individual organisms A-G. Scale bar: A & H = 10 µm, B-G = 5 µm.</p> <p>From:</p> <p>Schimak MP, Kleiner M, Wetzel S, Liebeke M, Dubilier N, Fuchs BM. 2015. MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells. Applied and Environmental Microbiology. Accepted manuscript posted online. doi:10.1128/AEM.02776-15</p>
Electrochemical Biosensing of Tuberculosis using CRISPR-Cas12a and redox-probe modified oligonucleotide
<p>We have submitted the manuscript in HELIYON </p> <p><span>Manuscript. Number: HELIYON-D-24-20798R3 </span></p> <p>Title: An electrochemical biosensor for the detection of tuberculosis specific DNA with CRISPR-Cas12a and redox-probe modified oligonucleotide. </p> <p>The dataset used in that study is available here. </p>
NMR spectra of A-rich oligonucleotides that pause polymerase progression
<p>1D proton NMR spectra of HHV6A-A and HPV18b-A in lithium cacodylate buffer with and without 100 mM KCl, recorded at 25 °C and 0 °C on 600 MHz NMR spectrometer.</p>
Data for: Oligonucleotide mapping via mass spectrometry to enable comprehensive primary structure characterization of an mRNA vaccine against SARS-CoV-2
<p>Oligonucleotide mapping via liquid chromatography mass spectrometry mass spectrometry (LC-MS/MS) was recently developed to support development of Comirnaty®, the world's first commercial mRNA vaccine which immunizes against the SARS-CoV-2 virus. Analogous to peptide mapping of therapeutic protein modalities, oligonucleotide mapping described here provides direct primary structure characterization of mRNA, through enzymatic digestion, accurate mass determinations, and optimized collisionally-induced fragmentation. Sample preparation for oligonucleotide mapping is a rapid, one-pot, one-enzyme digestion. The digest is analyzed via LC-MS/MS with an extended gradient and resulting data analysis employs semi-automated software. In a single method, oligonucleotide mapping readouts include a highly reproducible and completely annotated UV chromatogram with >98% sequence coverage and a microheterogeneity assessment of 5´ terminus capping and 3´ terminus poly(A) tail length. Oligonucleotide mapping was pivotal to ensure the quality, safety, and efficacy of mRNA vaccines by providing: confirmation of construct identity and primary structure and assessment of product comparability following manufacturing process changes. More broadly, this technique may be used to directly interrogate the primary structure of RNA molecules in general.</p>
Sequencing summaries & Nanopolish eventalign outputs for downstream analysis of yeast RNA and synthetic oligonucleotides
<p>This dataset contains:</p> <ol> <li>A set of text files from running the tool Nanopolish eventalign on several nanopore direct RNA sequencing data sets produced by Jay Hesselberth's lab at the University of Colorado (BioProject accession number <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA910992">PRJNA910992</a>), as well as external sequencing data sets from <a href="https://pubmed.ncbi.nlm.nih.gov/34893601/">PMID: 34893601</a> (synthetic oligonucleotides from Leger et al) and <a href="https://pubmed.ncbi.nlm.nih.gov/35252946/">PMID: 35252946</a> (yeast rRNA data from Stephenson et al).</li> <li>"Sequencing summary" files produced by MinKNOW, from nanopore sequencing of yeast mRNA and synthetic RNA oligos in the Hesselberth lab. We analyze these files in an associated manuscript to determine the "end status" of each read during the sequencing run.</li> </ol> <p>These files can be used as inputs to the R markdown documents at <a href="https://github.com/hesselberthlab/RNARePore">https://github.com/hesselberthlab/RNARePore</a> to reproduce the figures in the associated manuscript.</p>
Oligonucleotide Ligation Assay (OLA) Resistance Study
ClinicalTrials.gov study NCT01898754. IPD Sharing: NO. Countries: 1. Publications: 2.
Safety and Efficacy Study of Antisense Oligonucleotides in Duchenne Muscular Dystrophy
ClinicalTrials.gov study NCT00159250. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Data for: Oligonucleotide mapping via mass spectrometry to enable comprehensive primary structure characterization of an mRNA vaccine against SARS-CoV-2
Open the record for dataset details and reuse information.
Data from complex cation Λ-[Ru(1,4,5,8-tetraazaphenanthrene)2(dipyridophenazine)]2+ with the oligonucleotide d(TCGGCGCCGA) recorded as part of ongoing research
<p>Part of a data set recorded from a "standard crystal" of Λ-[Ru(1,4,5,8-tetraazaphenanthrene)2(dipyridophenazine)]2+ with the oligonucleotide d(TCGGCGCCGA) prepared according to protocol defined in: http://www.pnas.org/content/108/43/17610.abstract as part of ongoing research on beamline I04 at Diamond Light Source. Data consist of 3600 0.1 degree images recorded on a Pilatus 2 6M detector.</p>
Data For Mechanistic Insights into ASO-RNA Complexation: Advancing Antisense Oligonucleotide Design Strategies
<div>Available data from manuscript "Mechanistic Insights into ASO-RNA Complexation: Advancing Antisense Oligonucleotide Design Strategies"</div> <div> </div> <div>FOLDERS:</div> <div>1. STRUCTURES</div> <div>include starting, average and last snapshots</div> <div>2. RMSD</div> <div>rmsd for heavy atoms of whole complex, the hairpin (mRNA) and the aso</div> <div>3. RADGYR</div> <div>radius of gyration of heavy atoms for the whole complex</div> <div>4. RMSF</div> <div>rmsf by residue</div> <div>5. MOVIE</div> <div>trajectorie files (.tpr and .xtc) for heavy atoms each 0.5 ns</div> <div>6. INTERACTIONENERGIES</div> <div>1) ASO and hairpin nucleobases atoms (ASOBase-hairpinBase; specific interactions), 2) ASO and hairpin backbones atoms (ASOBac-hairpinBac; nonspecific), 3) ASO nucleobases and hairpin backbone atoms (ASOBase-hairpinBac), and 4) ASO backbone and hairpin nucleobases atoms (ASOBac-hairpinBase).</div> <div>7. HBOND</div> <div>hydrogen bonds between ASO and hairpin atoms and internal hydrogen bonds for the hairpin</div> <p>---------------------------------------------</p> <p>for more information contact johhor@chalmers.se</p>
NMR spectra of single-stranded and dimeric oligonucleotide constructs containing oxidative lesions
<p>NMR spectra of single-stranded (g- prefix) and dimeric (m- prefix) oligonucleotide constructs containing 8-oxoguanine (X) and dSpacer (S) lesions. Spectra were recorded on 600 and 800 MHz spectrometers. Oligonucleotides were dissolved in 50 mM KCl, 10 mM potassium phosphate buffer at pH 7, in 10% 2H2O.</p>
Accessible light-controlled knockdown of cell-free protein synthesis using phosphorothioate-caged antisense oligonucleotides (Raw data)
<p>Raw data for publication "Accessible light-controlled knockdown of cell-free protein synthesis using phosphorothioate-caged antisense oligonucleotides" (https://chemrxiv.org/engage/chemrxiv/article-details/6389f2dbe6f9a1754b2876d7)</p>
Clinical Trial of BP1001 (L-Grb-2 Antisense Oligonucleotide) in CML, AML, ALL & MDS
ClinicalTrials.gov study NCT01159028. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Pilot Study of EZN-2968, an Antisense Oligonucleotide Inhibitor of HIF-1alpha, in Adults With Advanced Solid Tumors With Liver Metastases
ClinicalTrials.gov study NCT01120288. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Phase I Study of RNA Oligonucleotide, MTL-CEBPA, Atezolizumab and Bevacizumab in Patients With Advanced Hepatocellular Carcinoma.
ClinicalTrials.gov study NCT05097911. IPD Sharing: NO. Countries: 1. Publications: 2.
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.