The primary meta-analysis (Stage 1) included 46 GWA studies of 133,653 individuals. The in-silico follow up (Stage 2) included 15 studies of 50,074 individuals. All individuals were of European ancestry and >99.8% were adults. Details of genotyping, quality control, and imputation methods of each study are given in Supplementary Methods Table 1-2 . Each study provided summary results of a linear regression of age-adjusted, within-sex Z scores of height against the imputed SNPs, and an inverse-variance meta-analysis was performed in METAL (http://www.sph.umich.edu/csg/abecasis/METAL/ ). Validation of selected SNPs was performed through direct genotyping in an extreme height panel (N=3,190) using Sequenom iPLeX, and in 492 Stage 1 samples using the KASPar SNP System. Family-based testing was performed using QFAM, a linear regression-based approach that uses permutation to account for dependency between related individuals29 (link), and FBAT, which uses a linear combination of offspring genotypes and traits to determine the test statistic30 (link). We used a previously described method to estimate the amount of genetic variance explained by the nominally associated loci (using significance threshold increments from P<5×10-8 to P<0.05)18 (link). To predict the number of height susceptibility loci, we took the height loci that reached a significance level of P<5×10-8 in Stage 1 and estimated the number of height loci that are likely to exist based on the distribution of their effect sizes observed in Stage 2 and the power to detect their association in Stage 1. Gene-by-gene interaction, dominant, recessive and conditional analyses are described in Supplementary Methods . Empirical assessment of enrichment for coding SNPs used permutations of random sets of SNPs matched to the 180 height-associated SNPs on the number of nearby genes, gene proximity, and minor allele frequency. GRAIL and GSEA methods have been described previously20 (link),21 . To assess possible enrichment for genes known to be mutated in severe growth defects, we identified such genes in the OMIM database (Supplementary Table 10 ), and evaluated the extent of their overlap with the 180 height-associated regions through comparisons with 1000 random sets of regions with similar gene content (±10%).
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Kaspar: Streamlining Research through AI-Driven Protocol Optimization
Kaspar, PubCompare.ai's innovative AI-powered platform, helps researchers optimize research protocols and enhance reproducibility.
By searching literature, preprints, and patents, Kaspar uses advanced AI comparisons to identify the best protocols and products, streamlining the research process and improving scientific outcomes.
Experiance the power of AI-driven protocol optimization with PubCompare.ai's Kaspar today, and take your research to new heights.
Kaspar, PubCompare.ai's innovative AI-powered platform, helps researchers optimize research protocols and enhance reproducibility.
By searching literature, preprints, and patents, Kaspar uses advanced AI comparisons to identify the best protocols and products, streamlining the research process and improving scientific outcomes.
Experiance the power of AI-driven protocol optimization with PubCompare.ai's Kaspar today, and take your research to new heights.
Most cited protocols related to «Kaspar»
Adult
Europeans
Genes
Genetic Diversity
Genome-Wide Association Study
Genotype
Iplex
kaspar
Metals
Single Nucleotide Polymorphism
Susceptibility, Disease
The neural progenitor cells isolated from the hippocampus of adult female Fischer 344 rats used in this work have been characterized previously (Gage et al., 1995 (link); Palmer et al., 1997 (link)). The whole brain–derived neural stem cells from P10 ICR mice were isolated and cultured according to the methods as described, with slight modifications. Cells were cultured as described previously (Ray et al., 1993 (link); Gage et al., 1995 (link)). Cells between passages 10 and 20 were used for in vitro differentiation analyses. To induce differentiation, cells were plated into 4-well chamber slides at a density of 55,000–75,000 cells/well and were allowed to proliferate in insulin-containing N2-supplemented (Invitrogen) DME:Ham's F12 (Omega Scientific) medium containing 20 ng/ml FGF-2 (PeproTech, Inc.) for 24 h. FGF-2 was then withdrawn and cells were subsequently treated with differentiation media. Differentiation conditions were either N2 medium with 1 μM RA (Sigma-Aldrich) and 1% FBS (Omega Scientific) for 4 d (mixed); 1 μM RA and 5 μM forskolin (Sigma-Aldrich) for 4 d (neuronal), or 50 ng/ml leukemia inhibitory factor (CHEMICON International, Inc.) and 50 ng/ml BMP2 (R&D Systems) for 6 d (astrocytic; Nakashima et al., 1999 (link)). For IGF induction experiments, cells were trypsinized, washed with 1× PBS, and plated into insulin-free N2 medium. Either 500 ng/ml human recombinant IGF-I or IGF-II (R&D Systems) or 500 ng/ml insulin (Sigma-Aldrich) was added for 4 d, except when indicated otherwise. In some cultures, 2.5 μM BrdU (Sigma-Aldrich) was added to label dividing cells, and 2 μM Q-VD-OPh (Enzyme Systems Products) was added to prevent apoptosis. Recombinant mouse Noggin (R&D Systems) was added in some cultures to a final concentration of 500 ng/ml.
Acrylamide
Adenoviruses
Cells
cesium chloride
Cloning Vectors
Electrophoresis
Phosphates
Plasmids
Pluronic F68
Saline Solution
Transfection
Transients
Virus
The TIMS module was incorporated in DIA-NN (version 1.8.1), which was used for the benchmarks and was operated with maximum mass accuracy tolerances set to 10 ppm for both MS1 and MS2 spectra. Protein inference was disabled for analyses using DDA-based spectral libraries, to use the protein groups therein. The --relaxed-prot-inf option was used for library-free processing of the leukemia dataset and the HeLa dilution series on timsTOF Pro 2, as this option implements a protein grouping strategy similar to the one used in FragPipe. Library generation was set to “IDs, RT and IM profiling”. MBR was enabled for the two-species human-yeast benchmark. When reporting protein numbers and quantities, the Protein.Group column in DIA-NN’s report was used to identify the protein group and the PG.MaxLFQ column (calculated using the MaxLFQ algorithm31 (link)) was used to obtain the normalized quantity. PSM tables (PSM.tsv files generated by Philosopher) contain accession numbers of all mapped proteins for each identified peptide, and this information was used to identify proteotypic peptides. In the benchmark for the numbers of unique proteins with the spectral library from the original dia-PASEF publication (Supplementary Fig. 2 ), the “Genes” column was used to count unique proteins (as gene products identified and quantified using proteotypic peptides only). For this, proteotypic peptides were annotated as such using the “Reannotate” option. Quantification mode was set to “Robust LC (high precision)”. All other settings were left default. Following previously published recommendations32 (link), and similarly to the previous dia-PASEF workflow14 (link), the software output was filtered at precursor q-value <1%. Global protein q-value <1% filter was also applied to all benchmarks, except for the HeLa dilution series on timsTOF Pro 2, wherein data were filtered for run-specific protein q-value <1%.
Of note, one of the two-proteome human-yeast benchmark files (200113_AUR_dia-PASEF_HY_200ng_15ng_90min_Slot1-5_1_1636.d) could not be read correctly due to data corruption, with all frames (i.e., dia-PASEF scans) from 55,877 onwards being discarded, which might have resulted in the benchmark results being very slightly worse.
For the FDR accuracy benchmark using a human—A. thalaina spectral library, Spectronaut 14.3.200701.47784 was run using default settings, except protein q-value filtering was set to 1 (i.e., 100%), and PTM localization was disabled. The Spectronaut 14.4 analysis of the leukemia dataset in directDIA mode was downloaded from thePXD022216 repository.
Of note, one of the two-proteome human-yeast benchmark files (200113_AUR_dia-PASEF_HY_200ng_15ng_90min_Slot1-5_1_1636.d) could not be read correctly due to data corruption, with all frames (i.e., dia-PASEF scans) from 55,877 onwards being discarded, which might have resulted in the benchmark results being very slightly worse.
For the FDR accuracy benchmark using a human—A. thalaina spectral library, Spectronaut 14.3.200701.47784 was run using default settings, except protein q-value filtering was set to 1 (i.e., 100%), and PTM localization was disabled. The Spectronaut 14.4 analysis of the leukemia dataset in directDIA mode was downloaded from the
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cDNA Library
Genes
HAVCR1 protein, human
HeLa Cells
Homo sapiens
Immune Tolerance
Leukemia
Peptides
Proteins
Proteome
Radionuclide Imaging
Reading Frames
Saccharomyces cerevisiae
Staphylococcal Protein A
Strains
Technique, Dilution
Most recents protocols related to «Kaspar»
The samples were genotyped by LGC Genomics in Hertfordshire. Primer designs for each SNP were prepared using the PrimerPicker software. LGC uses a proprietary genotyping method known as KBiosciences Competitive Allele Specific PCR (KASPar). A separate 5’ sequence was designed as a forward primer for each allele. The reaction mix includes complementary oligonucleotides for these 5’ tails bound either to FAM dye or Victoria fluorescent dye with different excitation and emission wavelengths. The fluorescent dye-bound oligonucleotides are matched by two complementary oligonucleotides bound to quenchers, which reduces the fluorescence emitted. As the DNA is amplified using polymerase chain reaction, more of the fluorescent dye-labelled oligonucleotides are combined, and uncoupled from their quenchers, producing the fluorescence. Each of the two homozygotes then have only one emission wavelength, whereas the heterozygotes has fluorescence at both wavelengths. ROX, also known as carboxyrhodamine, a fluorescent reference dye, was used as a reference to normalise the samples against to account for differences in starting amounts of DNA. Each pair of primers was tested against a panel of 50 samples to check for amplification and dimorphism. Samples were run on 1,384-well plates. Genotype calls were made using KlusterCaller software. Genotyping failed for rs2228570, with no results across the samples tested. This SNP was therefore excluded from the analyses.
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KASPar assays were performed for all the identified SNPs in the bmr transferred plants. KASPar genotyping assays were performed in parents and off-springs (F1 and BC1F1) at the four-leaf stage, using specific KASP markers i.e., BMR6-132 (snpSB00519_CALL) for bmr6 and BMR12-129 (snpSB00520_CALL) for bmr12. PCR products were size fractionated using capillary electrophoresis on an ABI3700 automatic DNA sequencer (Applied Biosystems USA). The KASPar SNP genotyping of sorghum samples was done at Intertek Hyderabad. KASPar-SNP markers for bmr12 allele resulted monomorphic. The designed bmr6 allele specific KASPar-SNP markers, on the other hand, were polymorphic and used as proxy to screen and classify the F1, BC1F1, and BC2F2 individuals into bmr6 heterozygotes, homozygotes, and Bmr; the BC2F2s derived from self-fertilizing true BC2F1s.
The above genomic DNA was analyzed for CAPS for bmr6 and bmr12, by PCR amplification using specific primers in a 20-μl reaction [50] . Further, the foreground marker-assisted selection across the donor-recurrent parent combinations was performed by identifying the presence of KASPar SNP (snpSB00519_CALL) BMR6-132 and KASPar SNP (snpSB00520_CALL) BMR12-129 markers in the target bmr6 and bmr12 loci on chromosomes 4 and 7, respectively [51] adapted from [52] . The primers used in this study are listed in Table 2.
The final volume of the reaction mixture used for genotyping was 10 μl which consists of 10-20 ng of DNA along with 1x KASP Reaction Mix, 1 μl of the assay mix containing the two allele-specific SNP primers as well as the common reverse primer. Fifteen minutes at 94°C, 10 touchdown cycles of 20 s at 94°C, 60 s at 63-55°C (dropping 0.8°C every cycle), and 30 cycles of 20 s at 94°C, 60 s at 55°C were the PCR cycling conditions.
The final volume of the reaction mixture used for genotyping was 10 μl which consists of 10-20 ng of DNA along with 1x KASP Reaction Mix, 1 μl of the assay mix containing the two allele-specific SNP primers as well as the common reverse primer. Fifteen minutes at 94°C, 10 touchdown cycles of 20 s at 94°C, 60 s at 63-55°C (dropping 0.8°C every cycle), and 30 cycles of 20 s at 94°C, 60 s at 55°C were the PCR cycling conditions.
The instructions for our open-ended questions stated the following: „Not only correct and reliable information can be found on the internet, but also a lot of false and/or misleading information (e.g., fake news). Please indicate up to 5 strategies or rules that you use to evaluate the accuracy and reliability of information on the internet or to identify false information.” In addition, the pre-service teachers were asked: “For each strategy/rule mentioned, please also indicate how relevant you consider the teaching of this strategy/rule to pupils in the classroom,” using a scale ranging from 0 (“not relevant at all”) to 6 (“very relevant”). The strategies were assessed in open statements. These open strategy statements were coded and summarized with the aid of a coding scheme following the standard approach by Mayring (2015) , as used in previous research (Kaspar et al., 2010 (link), 2014 (link); Hoss et al., 2021 (link)). In a first step, a category system was developed based on the first 10% of the data material by deriving categories from a total of 1,295 statements. This resulted in a category system comprising 17 categories. Subsequently, two persons coded the material independently after prior introduction to the categories. Inter-coder reliability was calculated by Kappa (Cohen, 1960 (link)), to ensure the applicability and objectivity of the categories. Agreement was very good across all categories with a minimum κ = 0.922. A consensual agreement was subsequently achieved through discussion in the very few cases of disagreement.
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To identify the crystalline structure, Fourier transform infrared (FTIR) spectroscopy in attenuated total reflection (ATR) mode Bruker Alpha II spectrometer with platinum ATR attachment and a diamond crystal was used. Spectra in the 400–1500 cm−1 range with a resolution of 1 cm−1 was collected to characterize the crystalline structure of the samples. The degree of β crystallinity phase in the samples was calculated as follows (Cai et al., 2017 (link); Xin et al., 2018 (link); Kaspar et al., 2020 (link)) the degree was calculated using Eq. 1 : where Aα and Aβ are the absorbance values at 763 cm−1 (CH2 in-plane bending or rocking and CF2 bending and skeletal bending) and 840 cm−1 (CH2 rocking and CF2 asymmetrical stretching), respectively.
To confirm the crystalline structure, X-ray diffractometer (XRD) X'Pert Pro PANalytical equipped with Cu/Kα radiation (wavelength 0.15418 nm) in the 2θ range of 0°–50° at a scanning speed of 0.1°/min, was used and crystalline content was analysed according to Eq.2 : where the Iα, Iγ, and Iβ correspond to the intensity peaks of the α, γ, and β phases, respectively. The XRD peaks for the monoclinic α phase are 18.7° (020), 19.8° (110), and 26.5° (021), while the 20.7° (110/200), 36.6° (101) and 56° (221) peaks correspond to the orthorhombic β phase peak, and the γ phase peak can be attributed to 40° (002) (Cai et al., 2017 (link); Xin et al., 2018 (link); Kaspar et al., 2020 (link)):
The average crystallite size (D) was identified using the Scherrer using Eq.3 : where λ is the wavelength of 1.54 Å, B is the Full Width at Half Maximum (FWHM), θ is Bragg’s and K is a constant 0.94 [54]. The obtained data was analysed using the GraphPad Prism 10 software.
To confirm the crystalline structure, X-ray diffractometer (XRD) X'Pert Pro PANalytical equipped with Cu/Kα radiation (wavelength 0.15418 nm) in the 2θ range of 0°–50° at a scanning speed of 0.1°/min, was used and crystalline content was analysed according to Eq.
The average crystallite size (D) was identified using the Scherrer using Eq.
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Top products related to «Kaspar»
Sourced in United Kingdom
KASPar assays are a type of genetic analysis tool developed by LGC. They are designed for the detection and genotyping of single nucleotide polymorphisms (SNPs) in DNA samples. KASPar assays utilize a proprietary technology that enables efficient and reliable SNP analysis.
Sourced in United Kingdom
The KASPar PCR SNP genotyping system is a laboratory equipment used for the detection and analysis of single nucleotide polymorphisms (SNPs) in DNA samples. It utilizes a fluorescence-based PCR (Polymerase Chain Reaction) technique to accurately determine the genetic makeup of specific DNA regions.
Sourced in United Kingdom, United States
The KASPar is a highly sensitive and specific DNA genotyping technology that enables accurate allelic discrimination. It utilizes competitive allele-specific PCR (KASP) for efficient and reliable genotyping of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels).
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The FlexiGene DNA Kit is a laboratory product designed for the purification of genomic DNA from a variety of sample types, including whole blood, buffy coat, cultured cells, and tissue. The kit utilizes a simple and efficient protocol to extract high-quality DNA, which can then be used for various downstream applications, such as PCR, sequencing, and genotyping.
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The QIAamp DNA Mini Kit is a laboratory equipment product designed for the purification of genomic DNA from a variety of sample types. It utilizes a silica-membrane-based technology to efficiently capture and purify DNA, which can then be used for various downstream applications.
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TaqMan assays are a type of real-time PCR (polymerase chain reaction) technology developed by Thermo Fisher Scientific. They are designed for sensitive and specific detection and quantification of target DNA or RNA sequences. TaqMan assays utilize fluorescent probes and specialized enzymes to generate a measurable signal proportional to the amount of target present in a sample.
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The 7500 Fast Real-Time PCR System is a thermal cycler designed for fast and accurate real-time PCR analysis. It features a 96-well format and supports a variety of sample volumes and chemistries. The system is capable of rapid thermal cycling and provides precise temperature control for reliable results.
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Retinoic acid is a chemical compound commonly used in laboratory settings. It is a form of vitamin A that plays a role in various biological processes. This product serves as a key reagent for researchers and scientists working in the fields of cell biology, developmental biology, and pharmacology.
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The LightCycler 480 is a real-time PCR instrument designed for quantitative nucleic acid analysis. It features a 96-well format and uses high-performance optics and detection technology to provide accurate and reliable results. The core function of the LightCycler 480 is to facilitate real-time PCR experiments through thermal cycling, fluorescence detection, and data analysis.
Sourced in Canada, United States
The Oragene DNA self-collection kit is a product from DNA Genotek that allows individuals to collect their own DNA sample. The kit includes a collection container and instructions for providing a saliva sample.
More about "Kaspar"
Kaspar, an innovative AI-driven platform developed by PubCompare.ai, is revolutionizing the way researchers optimize research protocols and enhance scientific reproducibility.
This cutting-edge technology leverages advanced artificial intelligence (AI) to scour literature, preprints, and patents, identifying the best protocols and products to streamline the research process and improve overall scientific outcomes.
Through its powerful AI-driven comparisons, Kaspar helps researchers navigate the vast landscape of available research tools and methodologies, including KASPar assays, KASPar PCR SNP genotyping systems, FlexiGene DNA Kits, QIAamp DNA Mini Kits, TaqMan assays, and the 7500 Fast Real-Time PCR System.
By drawing insights from these resources, Kaspar empowers researchers to make informed decisions, leading to more efficient and reliable experiments.
Kaspar's capabilities extend beyond protocol optimization, as it also provides valuable insights into the role of retinoic acid and its impact on various research fields.
Additionally, the platform integrates seamlessly with popular technologies like the LightCycler 480 and the Oragene DNA self-collection kit, further streamlining the research workflow.
Experiance the transformative power of Kaspar's AI-driven protocol optimization today and take your research to new heights.
Discover how this innovative platform can help you improve scientific reproducibility, enhance the efficiency of your experiments, and drive groundbreaking discoveries.
This cutting-edge technology leverages advanced artificial intelligence (AI) to scour literature, preprints, and patents, identifying the best protocols and products to streamline the research process and improve overall scientific outcomes.
Through its powerful AI-driven comparisons, Kaspar helps researchers navigate the vast landscape of available research tools and methodologies, including KASPar assays, KASPar PCR SNP genotyping systems, FlexiGene DNA Kits, QIAamp DNA Mini Kits, TaqMan assays, and the 7500 Fast Real-Time PCR System.
By drawing insights from these resources, Kaspar empowers researchers to make informed decisions, leading to more efficient and reliable experiments.
Kaspar's capabilities extend beyond protocol optimization, as it also provides valuable insights into the role of retinoic acid and its impact on various research fields.
Additionally, the platform integrates seamlessly with popular technologies like the LightCycler 480 and the Oragene DNA self-collection kit, further streamlining the research workflow.
Experiance the transformative power of Kaspar's AI-driven protocol optimization today and take your research to new heights.
Discover how this innovative platform can help you improve scientific reproducibility, enhance the efficiency of your experiments, and drive groundbreaking discoveries.