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Figure 3 in Determination of an efficient and reliable method for PCR detection of borrelial DNA from engorged ticks
Figure 3. Ratio of four different PCR types in presented ticks categories and isolation groups.
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>
Data from: Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab
<p>HER2/ERBB2 evaluation is necessary for treatment decision-making in breast cancer (BC), however current methods have limitations and considerable variability exists. DNA copy number (CN) evaluation by droplet digital PCR (ddPCR) has complementary advantages for HER2/ERBB2 diagnostics. In this study, we developed a single-reaction multiplex ddPCR assay for determination of ERBB2 CN in reference to two control regions, CEP17 and a copy-number-stable region of chr. 2p13.1, validated CN estimations to clinical in situ hybridization (ISH) HER2 status, and investigated the association of ERBB2 CN with clinical outcomes. 909 primary BC tissues were evaluated and the area under the curve for concordance to HER2 status was 0.93 and 0.96 for ERBB2 CN using either CEP17 or 2p13.1 as reference, respectively. The accuracy of ddPCR ERBB2 CN was 93.7% and 94.1% in the training and validation groups, respectively. Positive and negative predictive value for the classic HER2 amplification and non-amplification groups was 97.2% and 94.8%, respectively. An identified biological "ultrahigh" ERBB2 ddPCR CN group had significantly worse survival within patients treated with adjuvant trastuzumab for both recurrence-free survival (hazard ratio, HR: 3.3; 95% CI 1.1–9.6; <em>p</em> = 0.031, multivariable Cox regression) and overall survival (HR: 3.6; 95% CI 1.1–12.6; <em>p</em> = 0.041). For validation using RNA-seq data as a surrogate, in a population-based SCAN-B cohort (NCT02306096) of 682 consecutive patients receiving adjuvant trastuzumab, the ultrahigh-ERBB2 mRNA group had significantly worse survival. Multiplex ddPCR is useful for ERBB2 CN estimation and ultrahigh ERBB2 may be a predictive factor for decreased long-term survival after trastuzumab treatment.</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 and scripts from Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020
<p>Raw data and scripts used in the publication "<em>Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020 separator commenting unavailable</em>" in Eurosurveillance in 2022.</p> <p> </p> <p>https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.6.2100406</p>
PCR-GLOBWB 2 input files version 2017_11_beta_1
<p>Global extent input files at 5 arc-minute resolution and 30 arc-minute resolution for PCR-GLOBWB 2 (https://github.com/UU-Hydro/PCR-GLOBWB_model; Sutanudjaja et al., 2017).</p> <p>PCR-GLOBWB (PCRaster Global Water Balance) is a large-scale hydrological model intended for global to regional studies and developed at the Department of Physical Geography, Utrecht University (Netherlands).</p> <p>contact: Edwin Sutanudjaja (E.H.Sutanudjaja@uu.nl).</p> <p>Sutanudjaja, E. H., et al.: PCR-GLOBWB 2: a 5 arc-minute global hydrological and water resources model, submitted to Geosci. Model Dev. Discuss., 2017</p>
VDJ-PCR
<p><span>Supplementary Materials for doctoral thesis of Jingwei Zhang: sequence analysis of the rearranged immunoglobulin heavy chain loci of synL1E2 and convLCL cell lines.<span><br></span></span></p>
Fig.1 in Testing The Microsatellites-Pcr Markers For Genetic Diversity Research Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides G. O. Sars, 1894
Fig.1. Localities of sampling sities in the Latvian reservoirs.
Fig.1 in Protocol Optimization For Genomic Dna Extraction And Rapd-Pcr Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides
Fig.1. Localities of sampling sities in the Latvian reservoirs.
Figure 1 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 1. Prevalence of four different alleles of Pvmsp-3α (A, B, C and D) from PCR-RFLP
Figure 3 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 3. Prevalence of three different alleles of Pvmsp-3β (A, B, C) from PCR-RFLP.
Development of a specific PCR to detect thiocyanate-oxidizing Thioalkalivibrio strains in their environment
<p>Data repository for my thesis named 'Development of a specific PCR to detect thiocyanate-oxidizing <em>Thioalkalivibrio</em> strains in their environment' at the University of Amsterdam. The folder consists of 2 subfolders, namely the alignment, in both AA and NA forms, of the TcDH-sequences of the 10 Thioalkalivibrio strains, shown in <em>Figure 21</em> (1) and the alignment of the TcDH-sequences and names of the organisms used while making the phylogenetic tree of <em>Figure 2</em> (2).</p>
Database for comparison between Hybrid Capture and PCR techniques for HPV-HR detection
<p>This database displays the results from the HPV-HR detection with the gold standard technique Hybrid Capture 2 (HC2) and different PCR-based techniques. These results are compared in order to determine the degree of agreement between theses techniques. </p>
Splicing patterns of the Arabidopsis organellar rhomboid At1g74140 - Table S1 for primers used in the RT-PCR assays
<p>Extended Data for the publication: "Analysis of the <em>Arabidopsis</em> organellar rhomboid At1g74140 transcript population uncovered splicing patterns different from its close relative At1g74130"</p> <p>Supplementary Table S1 - List of At1g74140 primers used in the different RT-PCR assays. </p>
Figure 4 in Determination of genetic variations between Apodemus mystacinus populations distributed in Turkey inferred from mtDNA PCR-RFLP
Figure 4. UPGMA dendrogram of the composite data by combining cytb and D-loop regions.
Figure 1 in Investigation of GH and GHR Alu I gene polymorphisms on meat yields in Anatolian water buffalo breed using PCR-RFLP method
Figure 1. PCR products of exons 4 and 5 of the GH gene (428-bp band, M: 100-bp DNA ladder).
Fig. 1 in Taeniid cestodes in Tibetan foxes (Vulpes Ferrilata) detected by copro-PCR: Applications and challenges
Fig. 1. (continued).
Real-time RT-PCR datasets for the CEO study
<p>Real-time RT-PCR results of testing citrus essential oils for viroid transmission. </p> <p>Ct values of each run are listed in Excel sheet according to the respective experiment. </p>
Data from 'Sustainability in the laboratory: evaluating the reuseability of microtiter plates for PCR and fragment detection'
<p>This repository contains the data for the manuscript: Sustainability in the laboratory: evaluating the reuseability of microtiter plates for PCR and fragment detection.</p> <p>The script can be found here: https://github.com/AneLivB/SGP</p> <p><strong>Files: </strong></p> <p><strong>R15*_R*.csv</strong></p> <p>The processed data used for the script. All other files of the same name format contain the same elements!</p> <ul> <li> <p>Columns: Rack_location, ID, all loci</p> <ul> <li> <p>Rack_location: the location on the microwell plate the individual had in the wet lab</p> </li> <li> <p>ID: individual identification tag of the animal the DNA sample stems from</p> </li> <li> <p>_a and _b denotes the first and second allele of all loci</p> </li> </ul> </li> </ul> <p><strong>Mismatches</strong></p> <p>A dataframe created by the script and later used to calcualte per treatment single-locus genotype error rates.</p> <ul> <li> <p>Columns: Rack.1, Rack.2, Treatment, No..of.mistyped.alleles, No..of.mistyped.reactions, No..of.reactions, Allelic.error.rate, Genotype.error.rate</p> <ul> <li> <p>Rack.1: One of three racks (R154, R155, R156) from the standard protocol</p> </li> <li> <p>Rack.2: One of three racks (R154, R155, R156) from one of the other treatments (e.g. R154_R2, R154_R3, R154_R4)</p> </li> <li> <p>Treatment: One of three treatments (Internal control, Reused detection plate, Reused PCR plate)</p> </li> <li> <p>No..of.mistyped.alleles: Number of mismatched alleles within one treatment group, within a DNA plate</p> </li> <li> <p>No..of.mistyped.reactions: Number of mismatched single-locus genotypes within one treatment group, within a DNA plate</p> </li> <li> <p>No..of.reactions: Number of single-locus genotypes within one treatment group, within a DNA plate</p> </li> <li> <p>Allelic.error.rate: Error rate per allele</p> </li> <li> <p>Genotype.error.rate: Error rate per single-locus genotypes</p> </li> </ul> </li> </ul> <p><strong>model.mismatch.2.Rdata</strong></p> <p>RData file containing the model output.</p> <p> </p> <p><strong>Manuscript abstract: </strong></p> <p>Single-use plastics (SUPs) are indispensable in laboratory research, but their disposal contributes substantially to environmental pollution. Consequently, reusing common SUP items such as microtiter plates represents a promising strategy for improving laboratory sustainability. However, the key challenge lies in determining whether SUP reuse can be implemented without sacrificing data quality. To investigate this, we conducted a simple experiment to assess the impact of reusing microtiter plates on microsatellite genotyping accuracy. Plates previously used for PCR and fragment detection were cleaned using an environmentally friendly method and then reused. Our results indicate that, while reusing PCR plates significantly increases genotyping error rates due to residual DNA contamination, detection plates can be reused without compromising data quality. Our approach offers laboratories a practical and sustainable option for reducing SUP waste and costs while maintaining research integrity.</p>
Forest plot: Associations between BMI at baseline and pCR following NACT – stratification according to ER status.
<p>Forest plot: Associations between BMI at baseline and pCR following NACT – stratification according to ER status.</p>
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.