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Dataset PCR
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FIGURE 1. A, B in A multiplex PCR method for identification of two common true cutworm species (Lepidoptera: Noctuidae) tested in the central plain of Guilan province, Iran
FIGURE 1. A, B, Maize and green pepper fields damaged by true cutworm.
Fig. 3. Acanthamoeba specific PCR using JDP1 in First Report of a Case of Prostatitis Due to Acanthamoeba in a Dog
Fig. 3. Acanthamoeba specific PCR using JDP1/JDP2 primers. Lane 1: Molecular Weight Marker 100bp ladder; Lane 2: Prostate Fluid; Lane 3: Non-Nutrient Agar Amoebic Culture; Lane 4: Axenic culture; Lane 5: Positive control Acanthamoeba castellani Neff ATCC 30010 DNA; Lane 6: Negative control, bidistilled water.
Fig. 1 in Taeniid cestodes in Tibetan foxes (Vulpes Ferrilata) detected by copro-PCR: Applications and challenges
Fig. 1. Phylogram of Taenia species, which were found in China, especially in Tibetan Plateau, using the maximum likelihood method generated from partial cox1 (a) and nad1 (b) gene haplotypes. Isolates from Shiqu County were marked with ▴. Sequences from the referential T. polyacantha larva sample collected in Xinyuan County, Xinjiang Autonomous Region, China, shared the same haplotypes with published sequences from Finland marked with ☆. To each sequence, its accession number and geographic region were presented following the taeniid species name and haplotype number. Scale bar was represented in substitutions per nucleotide, and bootstrap values (with 1000 replicates) were marked at the nodes of branches.
Supplementary Figure 1. Comparison of diagnostic sensitivity of African swine fever virus (ASFV) real-time PCR kits using artificially spiked samples (ASSs)
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Data from: PCR-based isolation of multigene families: lessons from the avian MHC class IIB
The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multigene families, PCR-based approaches bear the often ignored risk of incomplete isolation of family members. This problem is most prominent in gene families with highly variable and thus unpredictable number of gene copies among species, such as in the major histocompatibility complex (MHC). In the present study we (i) report new primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds, and (ii) share our experience with isolating MHCIIB genes from an unprecedented number of avian species from all over the avian phylogeny. We report important and usually underappreciated problems encountered during PCR-based multigene family isolation, and provide a collection of measures to help significantly improving the chance of successfully isolating complete multigene families using PCR-based approaches.
Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing
<p><b>Introduction</b>: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. <span>Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited</span>. The aim of our study was to assess SalivaDirect as an alternative method for COVID-19 testing.</p> <p><b>Methods</b>: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using <i>RdRP</i> and <i>N1</i> gene targets in NPS and saliva respectively.</p> <p><b>Results</b>: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833–0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample (<i>p</i>=0.860). A highly significant correlation (r = 0.475, <i>p</i><0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens.</p> <p><b>Conclusions</b>: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Less invasive and accurate saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.</p>
DATABASE_Evaluation of the PCR-EIA
<pre>Database of HPV-HR detection results by INNOLIPA and PCR-EIA techniques</pre>
Figure 1 from: Hughes KW, Morris SD, Reboredo-Segovia A (2015) Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II. MycoKeys 10: 45-56. https://doi.org/10.3897/mycokeys.10.5126
Figure 1 - The ITS2 region of two haplotypes of Gymnopus dichrous: Haplotypes DI (represented by TENN68084) and DII (represented by TENN68078). The TC pair at position 15 and the indel at position 25 were used to determine which the haplotype was represented by the 5' end of a cloned sequence. Bases in red are points where DI and DII haplotypes differ in sequence and were used to determine if template switching had occurred in a cloned PCR product. Eight base pairs at which template switching can be detected are indicated by numbers 1-8. The possible area in which template switching (ts) could have occurred is indicated by vertical arrows and the number of observed template switching events is given above the vertical arrow. Bases that may be involved in intra-strand base pairing as determined by MFOLD are outlined with black boxes. Ambiguity codes indicate intraspecific variation.
Supplementary file 5. Primers for qRT-PCR
<p>Supplementary file 5. Primers for qRT-PCR</p> <p> </p>
Improving results from touch DNA evidence with optimized direct PCR methods
<p>Improved methods to generate high-quality DNA profiles from touch DNA samples are of considerable interest to forensic DNA laboratories. Direct polymerase chain reaction (PCR) amplification, a sample processing method in which samples are added directly to amplification reactions without prior purification or quantification, has been identified as a method that may improve the generation of genotyping data from such samples; however, laboratories in the United States are required to use standard DNA processing methods to process low-level sample types. In part, this is due to FBI Quality Assurance Standard (QAS) 9.4, which requires all unknown forensic samples to undergo human-specific DNA quantification prior to amplification of short tandem repeat (STR) loci. The goal of this 3-year study was to generate data in support of a reevaluation of QAS 9.4.</p> <p>In two phases, this study examined the following: direct PCR-compatible collection methods in conjunction with mock touch DNA evidence samples on a variety of substrates (Phase I), direct PCR of touch DNA samples that were stored at room temperature for up to six months after collection with the optimum methods identified in Phase I, and direct PCR of touch DNA samples that were re-sampled after initial processing. Nine collection methods and various substrates were examined in Phase I, and three time points were examined in Phase II. In both phases, two processing methods were used: standard processing samples were extracted, quantified, and amplified in accordance with the QAS; and direct PCR samples were directly amplified. All STR profiles were assessed for overall profile quality.</p> <p>This project was supported by Award No. 2019-DU-BX-0009, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice. The opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect those of the Department of Justice.</p>
RT-PCR raw data Zeng et al, 2023 Microorganisms
<p>RT PCR raw data linked to the publication Zeng et al, Microorganisms, MDPI, 2023</p>
Supplementary material 3 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
A specimen list of brittle star species collected from Sagami Bay in the last 10 years
Supplementary material 4 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
Supplementary images S1–S16
Supplementary material 2 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
Taxonomic notes for detected taxa
Supplementary material 1 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
A fasta file of 1,340 mitochondrial 16S rRNA gene sequences
Supplementary material 5 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
Additional data
Supplementary material 1 from: Röder N, Schwenk K (2023) Direct PCR meets high-throughput sequencing – metabarcoding of chironomid communities without DNA extraction. Metabarcoding and Metagenomics 7: e102455. https://doi.org/10.3897/mbmg.7.102455
Overview of chironomid size classes
Supplementary material 2 from: Röder N, Schwenk K (2023) Direct PCR meets high-throughput sequencing – metabarcoding of chironomid communities without DNA extraction. Metabarcoding and Metagenomics 7: e102455. https://doi.org/10.3897/mbmg.7.102455
Composition of the two artificial chironomid communities
Anamnesis data of PCR-positive dogs
<p>Data of anamnesis, clinical symptoms, and outcome of the disease. </p>
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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)
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.