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.
361
datasets available to search
ShareScore release 0.9.0
Dataset results
361 results for “quantitative PCR”
Fig. 1. A in A novel quantitative real-time PCR diagnostic assay for seal heartworm (Acanthocheilonema spirocauda) provides evidence for possible infection in the grey seal (Halichoerus grypus)
Fig. 1. A: graphical representation of cluster 20 (C20). B: representation of the selected contig and the sequence used to design the C20 quantitative real-time PCR assay. The forward primer is in bold, the reverse primer is indicated by a dotted underline, and the double-quenched probe is underlined.
Fig. 2. Standard curve generated using the log10 in A novel quantitative real-time PCR diagnostic assay for seal heartworm (Acanthocheilonema spirocauda) provides evidence for possible infection in the grey seal (Halichoerus grypus)
Fig. 2. Standard curve generated using the log10 of the ng of input A. spirocauda DNA plotted against Ct value. Unknown values are displayed as stars. For unknown samples, the total input DNA was 1 ng, which contains a mixture of seal DNA from the blood and A. spirocauda DNA. R2 = 0.985 for linear fit of standards. Curve is described by the equation y = −5.63x + 17.16, where y is the log (ng) and x is the Ct value. 95% confidence intervals are denoted by the dotted lines.
Fig. 2 in A novel quantitative real-time PCR diagnostic assay for fecal and nasal swab detection of an otariid lungworm, Parafilaroides decorus
Fig. 2. Standard curve based on sensitivity data. A 95% confidence interval for the linear regression model is shaded in grey.
Fig. 1. Repeat family selection for the P. decorus diagnostic assay. A in A novel quantitative real-time PCR diagnostic assay for fecal and nasal swab detection of an otariid lungworm, Parafilaroides decorus
Fig. 1. Repeat family selection for the P. decorus diagnostic assay. A. Number of sequencing reads for P. decorus compared to outgroup species reads for each repeat family (1–104) on a log scale. Arrows indicate repeat families with no reads from the outgroup species. Plot was made using Tableau Software, 2019. B. Within a cluster, reads with similar sequences are closer together. Edges connect a read with its closest match (creating a pair) and the length of this edge represents the amount of overlap between the reads. The mean edge width provides context for the lengths in the cluster, so in a cluster with a larger mean edge width the edges are actually longer than edges in a cluster with a smaller mean edge width. Reads therefore may be distant because of sequence divergence, or in the case of a long repeat (more than 150 base pairs), because of a lack of overlap between reads. However, because there will likely be continuous reads covering different regions of the repeat, these longer repeats should still appear as a tight, though possibly larger, cluster. Read dots that stray from the central cluster most likely represent sequence divergence. Higher density therefore indicates lower sequence divergence.
Supplemental files to: Probe-based quantitative PCR and RPA-Cas12a molecular diagnostics for detection of the tomato pest Phthorimaea absoluta (Lepidoptera: Gelechiidae)
Open the record for dataset details and reuse information.
Data from: Quantitative PCR as a marker for preemptive therapy and its role in therapeutic control in Trypanosoma cruzi/HIV coinfection
<p><strong>Background: </strong><em>Trypanosoma cruzi</em> and HIV coinfection can evolve with depression of cellular immunity and increased parasitemia. We applied quantitative PCR (qPCR) as a marker for preemptive antiparasitic treatment to avoid fatal Chagas disease reactivation and analyzed the outcome of treated cases.</p> <p><strong>Methodology:</strong> This mixed cross-sectional and longitudinal study included 171 Chagas disease patients, 60 coinfected with HIV. Of these 60 patients, ten showed Chagas disease reactivation, confirmed by parasites identified in the blood, cerebrospinal fluid, or tissues, 12 exhibited high parasitemia but no reactivation, and 38 had low parasitemia and no reactivation.</p> <p><strong>Results</strong>: We showed, for the first time, the success of the timely introduction of benznidazole in the non-reactivated group with high levels of parasitemia detected by qPCR and the absence of parasites in reactivated cases with at least 58 days of benznidazole. HIV+ and HIV+ without reactivation had a 4.0 – 5.1 higher chance of having parasitemia than HIV seronegative cases. A positive correlation was found between parasite and viral loads. Remarkably, treated <em>T. cruzi/</em>HIV-coinfected patients had 77.3% conversion from positive to negative parasitemia compared to 19.1% of untreated patients. Additionally, untreated patients showed ~13.6 times higher odds of having positive parasitemia in the follow-up period compared with treated patients. Treated and untreated patients showed no differences regarding the evolution of Chagas disease. The main factors associated with all-cause mortality were higher parasitemia, lower CD4 counts/µL, higher viral load, and absence of antiretroviral therapy.</p> <p><strong>Conclusion</strong>: We recommend qPCR prospective monitoring of <em>T. cruzi</em> parasitemia in HIV+ patients and point out the value of pre-emptive therapy for patients with temporary high parasitemia. In parallel, an early antiretroviral therapy introduction is advisable, aiming at viral load control, immune response restoration, and major survival. We also suggest an earlier antiparasitic treatment for all coinfected patients, followed by effectiveness analysis alongside antiretroviral therapy.</p>
Quantitative PCR from human genomic DNA: the determination of gene copy numbers for congenital adrenal hyperplasia and RCCX copy number variation
<p>The dataset is related a study in which we aimed to simultaneously assess the performance of 7 quantitative polymerase chain reaction (qPCR) assays for the gene copy number (GCN) determination of the genetic elements of RCCX copy number variation (CNV). A single laboratory method validations of duplex qPCR assays with hydrolysis probes on <em>CYP21A1P</em> and <em>CYP21A2</em> genes, which are responsible for congenital adrenal hyperplasia, were performed using 46 human genomic DNA samples. We also performed the verifications on 5 qPCR assays for the genetic elements of RCCX CNV such as <em>C4A</em> gene, <em>C4B</em>, gene, RCCX CNV breakpoint, HERV-K(C4) CNV deletion and insertion alleles. The dataset contains the data of genomic DNA samples, the raw quantification cycle values of all qPCR experiments, the peak heights and dosage quotient of multiplex ligation-dependent probe amplification (MLPA) experiments, and the detailed GCN results based on qPCR and MLPA. All other analyses are available in our publication under the same title.</p>
Data from: Quantitative PCR as a marker for preemptive therapy and its role in therapeutic control in Trypanosoma cruzi/HIV coinfection
Open the record for dataset details and reuse information.
Performance evaluation of a laboratory developed PCR test for quantitation of HIV-2 viral RNA
Open the record for dataset details and reuse information.
MicroRNA quantitative RT-PCR analysis of CMT1A Plasma
Open the record for dataset details and reuse information.
Data from: Quantitative PCR primer design affects quantification of dsRNA-mediated gene knockdown
RNA interference (RNAi) is a powerful tool for studying functions of candidate genes in both model and non-model organisms and a promising technique for therapeutic applications. Successful application of this technique relies on the accuracy and reliability of methods used to quantify gene knockdown. With the limitation in the availability of antibodies for detecting proteins, quantitative PCR (qPCR) remains the preferred method for quantifying target gene knockdown after dsRNA treatment . We evaluated how qPCR primer binding site and target gene expression levels affect quantification of intact mRNA transcripts following dsRNA-mediated RNAi. The use of primer pairs targeting the mRNA sequence within the dsRNA target region failed to reveal a significant decrease in target mRNA transcripts for genes with low expression levels, but not for a highly expressed gene. By contrast, significant knockdown was detected in all cases with primer pairs targeting the mRNA sequence extending beyond the dsRNA target region, regardless of the expression levels of the target gene. Our results suggest that at least for genes with low expression levels, quantifying the efficiency of dsRNA-mediated RNAi with primers amplifying sequences completely contained in the dsRNA target region should be avoided due to the risk of false negative results. Instead, primer pairs extending beyond the dsRNA target region of the mRNA transcript sequences should be used for accurate and reliable quantification of silencing efficiency.
Data from quantitative real-time PCR of corticotropin-releasing hormone and glucocorticoid receptor in the hippocampus and hypothalamus of rats subjected to midline fluid percussion injury or control sham surgery.
<p>These files contain all data from quantitative real-time PCR of corticotropin-releasing hormone (CRH) and glucocorticoid receptor (GR) measured in the hippocampus and hypothalamus of male and female rats. Rats were randomly assigned to a treatment group before the initiation of the study. Rats received a control sham surgery or were subjected to midline fluid percussion injury to induce a diffuse traumatic brain injury. Tissue biopsies were collected at 7 days post-injury and analyzed via quantitative real-time PCR. </p> <p> </p>
Supplementary data for "Validation of a quantitative PCR assay for detection of sugar kelp (Saccharina latissima) in coastal marine sediments"
<p>Raw data for a paper in preparation: "Validation of a quantitative PCR assay for detection of sugar kelp (Saccharina latissima) in coastal marine sediments".</p><p>Contains:</p><ol><li>Spreadsheet of curated raw data used to calculated <i>S. latissima</i> COI gene copy number per gram of dry sediment for a biomass spiking experiment to determine how gene copy number correlates with known amounts of added kelp biomass.</li><li>Spreadsheet of curated raw data from a field study looking at <i>S. latissima</i> gene copy numbers in field samples from the Damariscotta River estuary in Maine, from three sites, one under a small kelp farm, one under a site with a single kelp line, and another in a control site with no known influence of kelp farming activity.</li></ol>
Supplementary Figure S1 Identification the integrity of isolated endometrium and decidual tissues using quantitative PCR.
<p>Supplementary Figure S1 Identification the integrity of isolated endometrium and decidual tissues using quantitative PCR. The typical decidualization marker genes of <em>Dtprp</em> (A) and <em>Alpl</em> (B) were determined by qRT-PCR. (C) <em>ACTA2</em> mRNA levels of the smooth muscle maker gene was examined by qRT-PCR. Results were normalized to the housekeeping gene GAPDH and presented as the mean ± SD of three separate experiments, with different letters (a, b, c) indicating statistical difference (p < 0.05; one-way ANOVA and Tukey’s test).</p>
Quantitative real-time PCR assays Q2 for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates
<p>These are the data behind figures 2 to 7 in the paper: Brink AM, Kremp A and Gorokhova E (2024) Quantitative real-time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates. Front. Microbiol. 15:1421101. doi: 10.3389/fmicb.2024.1421101</p>
Fig. 3 in Establishment of conventional PCR and real-time PCR assays for accurate, rapid and quantitative authentication of four mistletoe species
Fig. 3. Sensitivity and amplification efficiency of qPCR assay using species-specific primers and serial dilutions of standard DNA. PCR cycling (A, C, E, G) and melting curve (B, D, F, H) analysis of primers specific for V. coloratum using VC-F3/R4 (A, B); T. sutchuenensis var. duclouxii using TS-F3/R4-1 (C, D), K. japonica using KJ-F5-1/R4 (E, F), and L. tanakae using LT-F5/R5-1 primers (G, H). Arrows indicate the amplification curves (A, C, E, G) of serial dilutions of standard DNA with NTC. Threshold was determined according to the Rotor-Gene Q series software (version 2.3.1) manual.
Fig. 2 in Establishment of conventional PCR and real-time PCR assays for accurate, rapid and quantitative authentication of four mistletoe species
Fig. 2. Sensitivity of multiplex PCR assay in conventional PCR. M: 100 bp DNA ladder. VC: V. coloratum. TS: T. sutchuenensis var. duclouxii. KJ: K. japonica. LT: L. tanakae. (+) means samples mixed different species used in PCR template. Hyphens and arrows indicate the sizes of DNA ladder and PCR products, respectively.
Fig. 4 in Establishment of conventional PCR and real-time PCR assays for accurate, rapid and quantitative authentication of four mistletoe species
Fig. 4. Analysis of commercial mistletoe products sold as leached tea in the Korean market using multiplex PCR assay. M: 100 bp DNA ladder. C1, VC_JM; C2, VC_GY; C3, TS_HR1; C4, TS_GC2; C5, KJ_SC1; C6, KJ_PS; C7, LT_GW; and C8, LT_JC (positive control). Lanes 1–16: Commercial food and herbal medicine products distributed as authentic mistletoe. Hyphens and arrows indicate the sizes of DNA ladder and PCR products, respectively. *, inauthentic products whose identity did not match the description on the label; **, inauthentic products whose identity matched the description on the label.
Quantitation of Bacteria Associated With Severe Periodontitis by Real -Time PCR Following Application of Diode Laser
ClinicalTrials.gov study NCT05222737. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Simultaneaous Detection of Quantitative Somatic Alterations Using the Qantitative Multiplex Pcr of Short Fluorescent Fragments Method (QMPSF) in Stage II-III Colon Cancer: a Prospective Study
ClinicalTrials.gov study NCT02110329. 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.