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47 results for “DNA amplification”
Detection of HER2+ Breast Cancer Cells using Bioinspired DNA-Based Signal Amplification
<p>Circulating tumor cells (CTC) are promising biomarkers for metastatic cancer detection and monitoring progression. However, CTC detection remains challenging due to their low frequency and heterogeneity. Herein, we report a bioinspired approach to detect individual cancer cells, based on a signal amplification cascade using a programmable DNA hybridization chain reaction (HCR) circuits. We applied this approach to detect HER2+ cancer cells using the anti-HER2 antibody (trastuzumab) coupled to initiator DNA eliciting a HCR cascade that leads to a fluorescent signal at the cell surface. At 4°C, this HCR detection scheme resulted in highly efficient, specific and sensitive signal amplification of the DNA hairpins specifically on the membrane of the HER2+ cells in a background of HER2- cells and peripheral blood leukocytes, which remained almost non-fluorescent. The results indicate that this system offers a new strategy that may be further developed toward an in vitro diagnostic platform for the sensitive and efficient detection of CTC.</p>
Fig. 2 in Optimisation Of Dna Extraction And Rapd-Pcr Amplification For Population Genetic Analysis Of Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera)
Fig. 2. RAPD fingerprints results from different samples of Daphnia cucullata with primers OPA-03 and OPA-05 (M- marker, 1-11 runners- different samples of Daphnia cucullata; 12- control) using RAPD-PCR 10 × Taq buffer with (NH4)2SO4.
Fig.1 in Optimisation Of Dna Extraction And Rapd-Pcr Amplification For Population Genetic Analysis Of Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera)
Fig.1. RAPD fingerprints results from different samples of Daphnia cucullata with primers OPA-03 and OPA-05 (M- marker, 1-16 runners- different samples of Daphnia cucullata; 17- control) using RAPD-PCR 10 × Taq buffer with KCl.
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp). in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp).
Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
<p>Biomonitoring surveys from environmental DNA make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species-level resolution. Here we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different long-fragment sequencing approaches using Oxford Nanopore sequencing coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion ('mitoenrichment'). A second enrichment approach takes advantage of the CRISPR-Cas9 targeted scission on previously dephosphorylated DNA ('targeted mitosequencing'). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17-12.33 % of sequences on target and a mean coverage ranging from 74.9 to 805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83-55 % of sequences on target and a 38 to 2123-fold mean coverage. This produced complete the mitogenome of species with homopolymeric regions, tandem repeats, and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA is possible and can be achieved with low computational resources in a cost-effective manner, opening the discovery of mitogenomes of non-model or understudied fish taxa to a broad range of laboratories worldwide.</p>
Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
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DNA origami signal amplification in lateral flow immunoassays
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Data from: Non-specific amplification compromises environmental DNA metabarcoding with COI
1. Metabarcoding extra-organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. However, choice of genetic marker and primer set is a critical consideration when designing experiments, especially so when developing community standards and legislative frameworks. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power, and predictable sequence variation, is the natural choice for many metabarcoding applications such as the bulk sequencing of invertebrates. However, the overall utility of COI for environmental sequencing of targeted taxonomic groups has yet to be fully scrutinised. 2. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve mitochondrial primer pairs from COI, cytochrome b, 12S and 16S, in terms of reference library coverage, taxonomic discriminatory power, and primer universality. We subsequently test in vitro three COI primer pairs and one 12S pair for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites in the English Channel and North Sea coast. 3. Our results show that for aqueous extra-organismal DNA at low template concentrations, both metazoan and fish-targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non-specific amplification of prokaryotic and non-target eukaryotic DNAs. 4. An ideal metabarcode would have an extensive reference library for which custom primer sets can be designed for either broad assessments of biodiversity or taxon specific surveys, but unfortunately, low primer specificity hinders the use of COI, while the paucity of reference sequences is problematic for 12S. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome-skimming existing tissue collections.
Cavity Lasing Characteristics of Thioflavin T and Thioflavin X in Different Solvents and Their Interaction with DNA for the Controlled Reduction of a Light Amplification Threshold in Solid-State Biofilms
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Supplementary material 1 from: Xu M, Liu Y, Möller E, LaGreca S, Moya P, Wang X, Timdal E, de Boer H, Barreno E, Wang L, Thüs H, Andrésson Ó, Magnússon KP, Ólafsdóttir ES, Heiðmarsson S (2023) Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland. MycoKeys 96: 57-75. https://doi.org/10.3897/mycokeys.96.100037
Multiple sequence alignment for fungal mtSSU primer design in the family Parmeliaceae (except for Usnea)
DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging
<p>Tiff images, single cell data, and cell masks for the publication "DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging". The code used to produce the results of this study is available at https://github.com/BodenmillerGroup/SABER-IMC_publication</p>
Data related to the manuscript "Reduced amplification by phi29 DNA polymerase in the presence of unbound oligos during rolling circle amplification"
<p>Raw data from AC susceptometry and processed data in excel sheets.</p>
DNA Amplification in Blastocoel Fluid
ClinicalTrials.gov study NCT04744844. IPD Sharing: YES. Countries: 1. Publications: 8.
Data from: Non-specific amplification compromises environmental DNA metabarcoding with COI
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Molecular diagnostics based on DNA amplification and magnetic sensor arrays
<p>On May 12, 2020, the third Scientific Online Lecture of the IPANEMA project was organized. The lecture has been given by INESC MN’s Researchers: Verónica Romão, Sofia Martins , Sara Viveiros, and Débora Albuquerque. Through this lecture, our researchers were able to get acquainted with the Molecular diagnostics based on DNA amplification and magnetic sensor arrays.</p>
Data related to the manuscript "Sequence-specific aggregation of magnetic nanoparticles and single-stranded DNA amplification products for detection of antibiotic resistance gene sul1."
<p>Absorbance and AC susceptometry raw and processed excel files used.</p>
Supplementary material 3 from: Xu M, Liu Y, Möller E, LaGreca S, Moya P, Wang X, Timdal E, de Boer H, Barreno E, Wang L, Thüs H, Andrésson Ó, Magnússon KP, Ólafsdóttir ES, Heiðmarsson S (2023) Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland. MycoKeys 96: 57-75. https://doi.org/10.3897/mycokeys.96.100037
Multiple sequence alignment for fungal mtSSU primer design of the genus Usnea
Supplementary material 2 from: Xu M, Liu Y, Möller E, LaGreca S, Moya P, Wang X, Timdal E, de Boer H, Barreno E, Wang L, Thüs H, Andrésson Ó, Magnússon KP, Ólafsdóttir ES, Heiðmarsson S (2023) Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland. MycoKeys 96: 57-75. https://doi.org/10.3897/mycokeys.96.100037
Priming sites for alternative mtSSU primers, Nanodrop results and in silico PCR amplicons
Video data describing bioluminescent detection of isothermal DNA amplification in microfluidic generated droplets and artificial cells
<p>Video data of loop-mediated isothermal nucleic acid amplification (LAMP) and bioluminescent assay in real time (BART) in microfluidicaly produced droplets. The videos are the data used to generate still images for figures in the source publication "Bioluminescent detection of isothermal DNA amplification in microfluidic generated droplets and artificial cells".</p> <p>Details of the videos acquisition parameters are as follows:</p> <ul> <li>Video 1: LAMP-BART droplets in tubing - no DNA template control (Figure 2a) (assay duration 600s, frames 1 per 10s, 60 frames, final</li> <li>Video 2 frames per second) Video 2: LAMP-BART droplets in tubing - positive DNA template control (Figure 2b) (assay duration 1800s, frames 1 per 10s, 180 frames, final video 10 frames per second)</li> <li>Video 3: LAMP-BART parked droplets (Figure 3) (assay duration 600s, frames 1 per 10s, 60 frames, final video 3.3 frames per second)</li> <li>Video 4: LAMP-BART DNA gradient in tubing (Figure 4) (assay duration 1800s, frames 1 per 10s, 180 frames, final video 10 frames per second)</li> <li>Video 5: LAMP-BART eDIBs (Figure 5) (assay duration 1570s, frames 1 per 10s, 157 frames, final video 5.2 frames per second)</li> <li>Video 6: One to four core LAMP-BART eDIBs (Figure 6) (assay duration 1200s, frames 1 per 10s, 120 frames, final video 5 frames per second)</li> </ul> <p>When referencing please use:</p> <p>Hardinge, P., Baxani, D. K., McCloy, T., Murray, J. A. H. & Castell, O. K. Bioluminescent detection of isothermal DNA amplification in microfluidic generated droplets and artificial cells. <em>Sci Rep</em> <strong>10</strong>, 21886 (2020).</p>
Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA
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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.