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Dataset results
78 results for “DNA recombination”
Recombination detection program (RDP4) results for ICMV and SLCMV DNA-B
<p>A DNA-B multiple alignment (Zenodo record 3964977) was scanned with RDP4.100 (D. Martin et al. 2015). Recombination breakpoints for events with statistical support from at least 5 of 7 methods were adjusted per the manual (high-confidence accepted events). A CSV file with the results for the accepted events was exported and then saved a second time with Excel to normalize format (a comma in between every column).</p> <p>Note added 2020-09-07: AJ575821 is listed in the files as ICMV based on its assignment in the NCBI Taxonomy database (taxa 341701 and 31600) but it is better classified as SLCMV.</p> <p>These results will be described in a manuscript by Crespo-Bellido et al.</p>
Increasing Recombinant Protein Production in E. coli via FACS-Based Selection of N-terminal Coding DNA Libraries
<p>Data for a manuscript to be deposited to the FEBS Journal. </p> <p>Abstract as deposited:</p> <p><span><span>We present a novel approach to modify N-terminal sequences of recombinant proteins to increase their production yield in <em><span>Escherichia coli</span></em>. Prior research has demonstrated a profound impact of a few nucleotides following the initiator codon (further to as N-terminal sequences) on their expression. Most of these investigations have been limited to selecting from a few rationally designed sequences. In contrast we used directed evolution-based methodology screening large numbers of diversified sequences derived from DNA libraries coding for the N-termini of investigated proteins. To facilitate the identification of cells with increasing expression of the target construct, we cloned a GFP gene at the C-terminus of the expressed genes and used fluorescent activated cell sorting (FACS) to separate cells based on their fluorescence. By following this systematic workflow, we successfully elevated the yield of soluble recombinant proteins of multiple constructs up to over 30-fold. </span></span></p>
Safety and Effectiveness of HIV-1 DNA Plasmid Vaccine and HIV-1 Recombinant Adenoviral Vector Vaccine in HIV-Uninfected, Circumcised Men and Male-to-Female (MTF) Transgender Persons Who Have Sex With
ClinicalTrials.gov study NCT00865566. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Recombination detection program (RDP4) results for ACMV and ACMBFV DNA-B
<p>A DNA-B multiple alignment (Zenodo record 3964979) was scanned with RDP4.100 (D. Martin et al. 2015). No events had statistical support from more than 4 of the 7 methods used to scan for signals of recombination.</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Recombination detection program (RDP4) results for EACMV-like DNA-B sequences (7 "species")
<p>A DNA-B multiple alignment (Zenodo record 3965023) was scanned with RDP4.97 (D. Martin et al. 2015). The input sequences belong to 7 “species”: CMMGV, EACMCV, EACMV, EACMKV, EACMMV, EACMZV, SACMV. Recombination breakpoints for events with statistical support from at least 5 of 7 methods were adjusted per the manual. These events were explicitly accepted, with the exception of one event which lost significance after adjustment of breakpoints. A CSV file with the results was exported and then saved a second time with Excel to normalize format (a comma in between every column).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Data from: DNA motifs are not general predictors of recombination in two Drosophila sister species.
Meiotic recombination is crucial for chromosomal segregation, and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes and Drosophila melanogaster exhibits a remarkable pattern. Recombination rates gradually decrease towards centromeres and telomeres, with a dramatic impact on levels of variation in natural populations. Two close sister species, D. simulans and D. mauritiana do not only have higher recombination rates, but also exhibit a much more homogeneous recombination rate that only drops sharply very close to centromeres and telomeres. Because certain sequence motifs are associated with recombination rate variation in D. melanogaster, we tested whether the difference in recombination landscape between D. melanogaster and D. simulans can be explained by the genomic distribution of recombination-rate associated sequence motifs. We constructed the first high-resolution recombination map for D. simulans based on 189 haplotypes from a natural D. simulans population, and searched for short sequence motifs linked with higher than average recombination in both sister species. We identified five consensus motifs significantly associated with higher than average chromosome-wide recombination rates in at least one species and present in both. Testing fine resolution associations between motif density and recombination, we found strong and positive associations genome-wide over a range of scales in D. melanogaster, while the results were equivocal in D. simulans. Despite the strong association in D. melanogaster, we did not find a decreasing density of these short-repeat motifs towards centromeres and telomeres. We conclude that the density of recombination-associated repeat motifs cannot explain the large-scale recombination landscape in D. melanogaster, nor the differences to D. simulans. The strong association seen for the sequence motifs in D. melanogaster likely reflects their impact influencing local differences in recombination rates along the genome.
Phase I Open-Label Study of Recombinant DNA Plasmid Vaccine, VRC-AVIDNA036-00-VP, Encoding for Influenza Virus H5 Hemagglutinin Protein Given Intradermally
ClinicalTrials.gov study NCT00489931. IPD Sharing: Not stated. Countries: 1. Publications: 3.
H7 Influenza Prime-Boost Regimens in Healthy Adults: Recombinant H7 DNA Plasmid Vaccine, VRC-FLUDNA071-00-VP, Administered Alone or With Monovalent Influenza Subunit Virion H7N9 Vaccine (MIV) as Prime
ClinicalTrials.gov study NCT02206464. IPD Sharing: Not stated. Countries: 1. Publications: 3.
HVTN Protocol 204 - A Phase II Clinical Trial to Evaluate the Safety and Immunogenicity of a Multiclade HIV-1 DNA Plasmid Vaccine, VRC-HIVDNA016-00-VP, Followed by a Multiclade Recombinant Adenoviral
ClinicalTrials.gov study NCT00125970. IPD Sharing: Not stated. Countries: 5. Publications: 7.
Safety of and Immune Response to a DNA Vaccine and a Recombinant HIV-1-MVA Vaccine, Separately and in Combination, in Healthy Adults
ClinicalTrials.gov study NCT00428337. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Data from: DNA motifs are not general predictors of recombination in two Drosophila sister species.
Open the record for dataset details and reuse information.
Safety and Immunogenicity of HIV DNA-C CN54ENV and Recombinant HIV CN54gp140 Vaccines in Healthy Volunteers
ClinicalTrials.gov study NCT02589795. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Recombinant DNA modification of gibberellin metabolism alters growth rate and biomass allocation in Populus
Open the record for dataset details and reuse information.
In vivo investigations of the effect of short- and long-term recombinant growth hormone treatment on DNA-methylation in humans
GEO Series GSE57107. Homo sapiens. 48 samples. Type: Methylation profiling by genome tiling array.
MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (RNA-Seq)
GEO Series GSE289796. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION [ATAC-Seq]
GEO Series GSE288585. Mus musculus. 27 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
In vivo investigations of the effect of short- and long-term recombinant growth hormone treatment on DNA-methylation in humans
GEO Series GSE57204. Homo sapiens. 54 samples. Type: Methylation profiling by genome tiling array.
Loss of DNA methylation affects recombination landscape in Arabidopsis
GEO Series GSE34173. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
Transient splicing inhibition causes persistent DNA damage and enhances chemotherapy vulnerability in homologous recombination proficient triple-negative breast cancer
GEO Series GSE271749. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
DNA cytosine methylation suppresses meiotic recombination at the sex-determining region (RNA-Seq)
GEO Series GSE245612. Chlamydomonas reinhardtii. 8 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
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OpenNeuro
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