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40 results for “Plasmid sequences”
Genomes plasmids MDR B. fragilis ONT sequence read files in fastq format
<p>Supporting data for the manuscript <em>Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids.</em></p> <p>Oxford Nanopore reads demultiplexed with <a href="https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=2ahUKEwjNjqL5tY7iAhUawMQBHZHfDasQFjAAegQIAhAB&url=https%3A%2F%2Fgithub.com%2Frrwick%2FDeepbinner&usg=AOvVaw0wikvIUagLuFV38CwKZtia">Deepbinner</a> v0.2.0 and base-called (with demultiplexing) using Albacore v2.3.3. Barcodes and adapters were removed with <a href="https://github.com/rrwick/Porechop">Porechop</a> v0.2.4 with the --discard_middle option.</p> <p>Data from each isolate was produced from two runs per isolate. Data for the individual runs are included here. They can easily be concatenated eg with cat. Runs are named TVS_01,. TVS_02, TVS_03 and TVS_04.</p> <p>Fast5 (only demultiplexed with deepbinner and basecalled with albacore) as well as illumina reads and genome assemblies can be found via the NCBI bioproject accessions:</p> <p>Isolates, NCBI bioproject accession no:</p> <p>CCUG4856T, <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA525024">PRJNA525024</a></p> <p>BFO17, <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA244943">PRJNA244943</a></p> <p>BFO18, <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA244944">PRJNA244944</a></p> <p>S01, <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA244942">PRJNA244942</a></p> <p>BFO42, <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA253771">PRJNA253771</a></p> <p>BFO67, <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA254401">PRJNA254401</a></p> <p>BFO85, <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA254455">PRJNA254455</a></p> <p> </p> <p><strong>md5sum's (also found in the file md5.md5):</strong></p> <p>135d0570a1e49e25c8fde59f321cca68 BFO17_TVS_03_99377.barcode02_trimmed.fastq.gz<br> 3c6ca800a1f735937c0cffccd263fb82 BFO18_TVS_01_97673.barcode03_trimmed.fastq.gz<br> dc37823950f529d3a859b7a7c514af8c BFO18_TVS_03_99377.barcode03_trimmed.fastq.gz<br> abd707404f9ebbc38652e45ed378ca21 BFO42_TVS_02.barcode10_trimmed.fastq.gz<br> 9761e9ab082e276624c5778dcbeaffd2 BFO42_TVS_04.barcode10_trimmed.fastq.gz<br> ffc27009c0f7fead1af84ce045dbe5f3 BFO67_TVS_02.barcode09_trimmed.fastq.gz<br> 06c363a7feeeb88f9d195b3769b37f2b BFO67_TVS_04.barcode09_trimmed.fastq.gz<br> 5553c95cc98f4b9d4cfb38c4f8f8f037 BFO85_TVS_02.barcode08_trimmed.fastq.gz<br> b1a8013cba7a079cee6d3bdd6cd97ff2 BFO85_TVS_04.barcode08_trimmed.fastq.gz<br> 8169225219a5fb20935d5f0304aa80c5 CCUG4856T_TVS_01_97673.barcode01_trimmed.fastq.gz<br> a509b0ae912a798a91e677795198c1c6 CCUG5846T_TVS_03_99377.barcode01_trimmed.fastq.gz<br> 8a9d2eb8b626a6e87ed267d31aa220e3 S01_TVS_01_97673.barcode04_trimmed.fastq.gz<br> 69e239a17becc25a4f103dfc3bf5886a S01_TVS_03_99377.barcode04_trimmed.fastq.gz</p>
All plasmid sequences
<p>Here are the full sequences of 33 plasmids used in the following BioRxiv manuscript: https://doi.org/10.1101/2021.09.15.460454</p> <p> </p>
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>S1 Data</p> <p>Dataset including the discovered CRISPR spacers, direct repeats, protospacers, co-occurrence-based spacer clustering results, predicted protein sequences, built HMMs, database comparison results, phylogenetic analysis results, predicted targeting hosts, and CRISPR-targeted TR sequences.</p>
Nanopore sequencing of plasmid cleavage fragments produced with type III CRISPR-associated nucleases NucC, Can1 and Can2
<p>Included datasets were generated in the study "<strong>Sequence-specific capture and concentration of viral RNA </strong><strong>by type III CRISPR system enhances diagnostic"</strong> by Nemudraia et al., 2022</p> <p> </p> <p>For questions contact: Artem Nemudryi (artem.nemudryi@gmail.com) or Blake Wiedenheft (bwiedenheft.com)</p>
.bam alignment files of Illumina and ONT sequencing of pREF plasmid
<p>The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed <em>pREF</em>, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The <em>pREF</em> sequence encodes 21 synthetic genes that can be <em>in vitro</em> transcribed into spike-in mRNA controls, and <em>in vitro</em> translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of <em>pREF</em> in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, <em>pREF</em> can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides the first universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.</p>
Plasmid Sequences for Brophy et al., 2022: Synthetic genetic circuits as a means of reprogramming plant roots
<p>Plasmid Sequences for Brophy et. al. 2022: Synthetic genetic circuits as a means of reprogramming plant roots</p>
Human intestinal Bacteria Collection (HiBC): Plasmids sequences
<p>The <a href="https://hibc.rwth-aachen.de/" target="_blank" rel="noopener">Human intestinal Bacteria Collection (HiBC)</a> is a collection of bacterial strains, isolated from the human gut for which 16S rRNA gene sequences, genome sequences and culture conditions are made available to the research community. In addition to previously described bacteria, we include strains that represent novel species which have been taxonomically described and validly named, or will be in the future. This collection will be updated regularly.</p> <p>This dataset includes the plasmids sequences of some of the isolates in the FASTA nucleotide format.</p>
Raw data for whole plasmid and whole genome sequencing
<p>Original data for plasmid and genomic DNA sequencing in the paper: Tailoring Microbial Fitness Through Computational Steering and CRISPRi-Driven Robustness Regulation</p>
MinION plasmid deep long read sequencing for sequence verification
<p>We sequenced four plasmid constructs, each with a whole MinION flowcell, for use in developing and testing a sequence verification procedure. The resulting pipeline can sequence verify plasmid constructs, generating a consensus sequence with associated confidence of each base, adhering to strict acceptance criteria . The data contained herein are a subset of the complete data; 30 fast5 files for each plasmid, to be used as example data.</p> <p> </p> <p>datHL_001519: BCRxV.TF.1<br> datHL_001521: BCRxV.VSVG.1<br> datHL_001617: BCRxV.GagPolRev.1<br> datHL_001620: BCRxV.VSVG.1_mutant</p>
Read coverage information for analysis missing plasmid sequences
<p>This file contains two directories: read_coverage, and read_coverage_contigs. This directories should be decompressed and located within ecoli-binary-classifier/2021_11_missing_sequences_analysis/results/ in order to reproduce results described the in the mansucript.</p>
.bam alignment files of Illumina and ONT sequencing of pREF plasmid
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Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids (Source Data)
<p>Source data for Chemical Science paper "Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids" DOI: 10.1039/D3SC02761A</p>
Sequence and functional analyses of native plasmids from plant pathogenic Gammaproteobacteria: comparative genomics, conjugative mobilization and fitness effects
<p>These data tables are part of the Supplementary Material for Chapter I of the thesis titled <em>"Sequence and Functional Analyses of Native Plasmids from Plant-Pathogenic Gammaproteobacteria: Comparative Genomics, Conjugative Mobilization, and Fitness Effects."</em></p>
Plasmid sequence of cpX
<p>Sequence of plasmid </p>
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>Supplementary Table 2-1. Samples and assembly summary <br> Supplementary Table 2-2. CRISPR-targeted TR sequence summary</p>
Plasmid sequences for the paper "A FRET based biosensor for measuring Gα13 activation in single cells"
<p>Plasmid sequences for the paper "A FRET based biosensor for measuring Gα13 activation in single cells"</p>
Plasmid sequences for: Recombinant venom proteins in insect seminal fluid reduces female lifespan
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Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
GEO Series GSE108890. Zymomonas mobilis subsp. mobilis. 17 samples. Type: Expression profiling by high throughput sequencing.
Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria
GEO Series GSE255663. Escherichia coli; Citrobacter freundii; Klebsiella pneumoniae. 55 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing Analysis of Transcriptomes of the HEK293T-Cas9 cells transfected with plasmid containing programmed scaffold RNA
GEO Series GSE143880. Homo sapiens. 5 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.
Annotated Behaviour and Observability Dataset (ABODe)
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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.