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11 results for “DNA contamination”
Data for "Influences of Glyphosate Contaminations and Concentrate Feed on Performance, Blood Parameters, Blood Cell Functionality and DNA Damage Properties in Fattening Bulls"
<p>The deposited data consist of three data tables and three tables containing legends for the data:</p> <p><a href="https://zenodo.org/api/files/afb9373a-d44c-4441-ba97-052c0b6ec1b6/oneTimepoint.txt">oneTimepoint.txt</a> contains data from statistical tests within one timepoint; <a href="https://zenodo.org/api/files/afb9373a-d44c-4441-ba97-052c0b6ec1b6/oneTimepoint_legend.txt">oneTimepoint_legend.txt</a> contains the corresponding legend.</p> <p><a href="https://zenodo.org/api/files/afb9373a-d44c-4441-ba97-052c0b6ec1b6/threeTimepoints.txt">threeTimepoints.txt</a> contains data from statistical tests inclduing three distinct timepoints; <a href="https://zenodo.org/api/files/afb9373a-d44c-4441-ba97-052c0b6ec1b6/threeTimepoints_legend.txt">threeTimepoints_legend.txt</a> contains the corresponding legend.</p> <p><a href="https://zenodo.org/api/files/afb9373a-d44c-4441-ba97-052c0b6ec1b6/Performance.txt">Performance.txt</a> contains data from statistical tests inclduing two time periods in fattening; <a href="https://zenodo.org/api/files/afb9373a-d44c-4441-ba97-052c0b6ec1b6/Performance_legend.txt">Performance_legend.txt</a> contains the corresponding legend.</p>
Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses.
Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
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Supplementary Materials for: Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China
<p>Supplementary Materials for</p><p><strong>Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China</strong></p><p>Adrian Jones, Daoyu Zhang, Steven E. Massey, Yuri Deigin, Louis R. Nemzer, Steven C. Quay</p>
Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA
<p>The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains (Mathieson et al., 2015; Narasimhan et al., 2019) or sediments (Vernot et al., 2021; Wang et al., 2021; Zavala et al., 2021) in single studies. Yet demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here we explore the possibility of improving the economics of sample preparation via multiplex capture, i.e. the hybridization capture of pools of double-indexed ancient DNA libraries. We demonstrate that this strategy is feasible for small genomic targets, such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post-capture amplification to avoid index swapping by jumping PCR, which manifests as cross-contamination in resulting sequence data. We also show that the re-amplification of double-indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross-contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384-well format that are compatible with single- and multiplex capture and effectively suppress cross-contamination and artefact formation. Last, we provide a simple computational method for quantifying cross-contamination due to index swapping in double-indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross-contamination. </p>
Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA
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Data from: Modified low-salt CTAB extraction of high-quality DNA from contaminant rich tissues
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Accumulation of airborne, eukaryotic environmental DNA contamination: Raw sequencing data and demultiplexing info
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Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA
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Somatic cell contamination in sperm human DNA methylatoin studies
GEO Series GSE108058. Homo sapiens. 30 samples. Type: Methylation profiling by genome tiling array.
DNA methylation profile of the Mediterranean fin whale (Balaenoptera physalus) exposed to organochlorine contaminants.
GEO Series GSE153525. Balaenoptera physalus. 6 samples. Type: Methylation profiling by high throughput sequencing.
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