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29 results for “primer sequences”
Sequence data for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers"
<p>Sequence data (Illumina MiSeq runs) for the article "Targeted reduction of highly abundant transcripts with pseudo-random primers". File names indicate unique run identifiers. In the manuscript, shorter names are used:</p> <ul> <li>NC12: 140602_M00528_0019_000000000-A88YD</li> <li>NC17: 140918_M00528_0047_000000000-A8GHU</li> <li>NC22b: 141105_M00528_0062_000000000-AAPC2</li> <li>NCki: 140207_M00528_0069_000000000-A5TY9</li> </ul> <p> </p>
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).
Text-fig. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114. 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. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114.
APPENDIX 10. — Additional ITS sequences used for Appendix 9 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
APPENDIX 10. — Additional ITS sequences used for Appendix 9, approximately in the same order. Abbreviations: MO, Mushroom Observer (https://mushroomobserver.org); iNAT, iNaturalist (https://www.inaturalist.org/observations).
Data for Coral Growth and Sequences for Cyclin-E and G3P Primers for Orbicella faveolata
<p>Cyclin-E and glyceraldehyde 3-phosphate dehydrogenase primer sets were constructed using Primer3 from an annotated<br> transcriptome (Polato et al., 2011). For each sample and gene, reactions were performed in triplicate on a Step One Plus qPCR<br> machine (Applied Biosystems, Waltham, MA), using cDNA of <em>Orbicella faveolata</em> (Ellis & Solander, 1786) as a template. Singlepeak melt curve analysis was performed to test for nonspecific amplification products, but limited sample prevented primer<br> efficiency analysis. To verify primer specificity, the two primers were tested on cDNA from <em>Casseopia xamachana</em>, with no<br> amplification being observed.</p>
Nucleotide sequence database of Copper-containing membrane monooxygenases genes for analysing primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia oxidising Nitrospira
<p>Nucleotide sequences of 487 Cu-mmo genes, including amoA comammox clade A and clade B, amoA ammonia oxidizing bacteria as well as other Cu-mmo genes.</p>
Primers for whole genome sequencing of the Sars-Cov-2 virus
<p>Here is the primer sequence for amplification and sequencing of the whole genome of the Sars-Cov-2 virus.</p>
Primer sequences for H3N2 canine influenza virus full-length amplification, polymerase activity assay, and rescue
<p><span>Influenza A viruses in animal reservoirs repeatedly cross species barriers to infect humans. Once an animal-borne virus with novel antigenicity acquired the efficient human-to-human transmissibility, it will become epidemic in the population. Dogs are the closest animal companions to humans, and canine respiratory tract expresses both SAα2,3-(avian type) and α2,6-Gal (human type) receptors. However, the role of dogs in the ecology of influenza viruses is unclear. H3N2 avian influenza viruses were transmitted to dogs around 2006 and have formed stable lineages. The long-term epidemic of avian-origin H3N2 virus in canines offers the best models to investigate the effect of dogs on the evolution of influenza viruses. Here, we carried out a systematic and comparative identification of the biological characteristics of H3N2 canine influenza viruses (CIVs) isolated in worldwide</span> <span>over 10 years. We found that during the adaptation of H3N2 CIVs to dogs, H3N2 CIVs became to recognize the human-like SAα2,6-Gal receptor, gradually increased HA acid stability and replication ability in human airway epithelial cells, and acquired a 100% transmission rate via respiratory droplet in ferret model, which were essential hallmarks of being adapted to humans. We also identified that the frequency of substitutions related to human adaptation has gradually increased in H3N2 CIVs and determined four cumulative molecular changes responsible for the increased airborne transmission ability in ferrets. Our results suggested that canines may serve as an intermediate for the adaptation of avian influenza virus to humans. Continuous surveillance coordinated with risk assessment for CIVs is necessary.</span></p>
Dataset for: How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes
<p><span>For nearly 15 years now, environmental DNA</span><span> has demonstrated</span><span> its effectiveness in monitoring biodiversity. Methodological and technical improvements have significantly enhanced the field. However, the effect of factors such as sequence coverage, bioinformatic filtration and primer choice have been less explored or need to be optimized according </span><span>to </span><span>specific survey objectives and </span><span>study </span><span>site characteristics. We evaluated these factors </span><span>to </span><span>help optimize monitoring fish biodiversity in North American temperate lakes. We sampled water for fish community eDNA analysis in 12 lakes from southwestern Québec, Canada. The lakes were selected to encompass a wide range of surface areas and species richness. We sampled water from a total of </span><span>520</span><span> sites (25 to 50 per lake) and analyzed three mitochondrial DNA regions (12S rRNA; 16S rRNA; and cytb) using NovaSeq</span><span> sequencing. Our results, based on rarefied count matrices (from a sequencing depth of 100,000 to a minimum </span><span>depth </span><span>of 1,000 reads per sample), </span><span>showed</span><span> that </span><span>keeping only</span><span> species </span><span>in each sample if they</span><span> represented </span><span>at least one thousandth (species </span><span>minimum </span><span>read proportion threshold =</span><span> 0.001</span><span>)</span><span> of the </span><span>sample's</span><span> reads was adequate to remove false positives </span><span>and had a limited negative</span><span> impact on true positives</span><span> with low read counts. The</span><span> sequencing depth </span><span>was found to have</span><span> a negligible impact </span><span>on the accuracy</span><span> of fish </span><span>community assessment in a given lake. With the same sequencing depth and a complete local reference database for each primer set, </span><span>a single primer set </span><span>produced</span><span> similar species richness medians than the combination of two or three primer sets. Overall, 12S and 16S detected more species and provided more consistent community profiles than cytb. </span><span>Based on our observations, we suggest using the 12S MiFish-U primer set and applying a minimum proportion of 0.001 reads per species and site to monitor north-temperate lentic freshwater fish communities.</span></p>
Primer sequences for H3N2 canine influenza virus full-length amplification, polymerase activity assay, and rescue
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Supplementary table, figures and DNA sequences of sorghum gene models SbiRTx430.01G455400 and SbiRTx.02G006600 that feature primers, gRNAs and indels created
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Dataset for: How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes
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Sequences of primers used for RT-qPCR assay
<p>the detailed sequences of the primers of tsRNAs and mRNAs used for RT-qPCR assay</p>
Data from: Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family
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Data from: Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing
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Data from: Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods
The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer–template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator-specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 °C annealing temperature and 40 cycles) and high-throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer–template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer–template mismatches explained most of the variation (~3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.
Data from: Diversity measures in environmental sequences are highly dependent on alignment quality—data from ITS and new LSU primers targeting basidiomycetes
The ribosomal DNA comprised of the ITS1-5.8S-ITS2 regions is widely used as a fungal marker in molecular ecology and systematics but cannot be aligned with confidence across genetically distant taxa. In order to study the diversity of Agaricomycotina in forest soils, we designed primers targeting the more alignable 28S (LSU) gene, which should be more useful for phylogenetic analyses of the detected taxa. This paper compares the performance of the established ITS1F/4B primer pair, which targets basidiomycetes, to that of two new pairs. Key factors in the comparison were the diversity covered, off-target amplification, rarefaction at different Operational Taxonomic Unit (OTU) cutoff levels, sensitivity of the method used to process the alignment to missing data and insecure positional homology, and the congruence of monophyletic clades with OTU assignments and BLAST-derived OTU names. The ITS primer pair yielded no off-target amplification but also exhibited the least fidelity to the expected phylogenetic groups. The LSU primers give complementary pictures of diversity, but were more sensitive to modifications of the alignment such as the removal of difficult-to align stretches. The LSU primers also yielded greater numbers of singletons but also had a greater tendency to produce OTUs containing sequences from a wider variety of species as judged by BLAST similarity. We introduced some new parameters to describe alignment heterogeneity based on Shannon entropy and the extent and contents of the OTUs in a phylogenetic tree space. Our results suggest that ITS should not be used when calculating phylogenetic trees from genetically distant sequences obtained from environmental DNA extractions and that it is inadvisable to define OTUs on the basis of very heterogeneous alignments.
COI sequences used in primer design
<p>COI sequences used for designing specific primers for <em>Garra cambodgiensis</em></p>
Supplementary Table S1. Primer sequence information for RT-qPCR used in this study.
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Data from: Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods
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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.