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2,848 results for “sequence data”
Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300–400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.
Data from: Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations
Indexing individual template molecules with a unique identifier (UID) before PCR and deep sequencing is promising for detecting low frequency mutations, as true mutations could be distinguished from PCR errors or sequencing errors based on consensus among reads sharing same index. In an effort to develop a robust assay to detect from urine low-abundant bladder cancer cells carrying well-documented mutations, we have tested the idea first on a set of mock templates, with wild type and known mutants mixed at defined ratios. We have measured the combined error rate for PCR and Illumina sequencing at each nucleotide position of three exons, and demonstrated the power of a UID in distinguishing and correcting errors. In addition, we have demonstrated that PCR sampling bias, rather than PCR errors, challenges the UID-deep sequencing method in faithfully detecting low frequency mutation.
Data from: Random-sequence genetic oligomer pools display an innate potential for ligation and recombination
Recombination, the exchange of information between different genetic polymer strands, is of fundamental importance in biology for genome maintenance and genetic diversification mediated by dedicated recombinase enzymes. Here, we describe a pervasive non-enzymatic capacity for recombination (and ligation) in random-sequence genetic oligomer pools. Specifically, we examine random and semi-random eicosamer (N20) pools of RNA, DNA and the unnatural genetic polymers ANA (arabino-), HNA (hexitol-) and AtNA (altritol-nucleic acids). While DNA, ANA and HNA pools proved inert, RNA and AtNA pools displayed diverse modes of spontaneous intermolecular recombination, connecting recombination mechanistically to the vicinal ring cis-diol configuration shared by RNA and AtNA. Thus, the chemical constitution that renders both susceptible to hydrolysis emerges as the fundamental determinant of an innate capacity for recombination, which is shown to enable a concomitant increase in compositional, informational and structural pool complexity and hence evolutionary potential.
Chart 1 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Chart 1 Continued.
Chart 1 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Chart 1 Continued.
Chart 1 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Chart 1 Continued.
Figure 5 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 5 Continued.
Figure 4 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 4 Continued.
Figure 5 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 5 Continued.
Figure 5 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 5 Continued.
Figure 4 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 4 Continued.
Figure 4 from: Kavanaugh DH, Maddison DR, Simison WB, Schoville SD, Schmidt J, Faille A, Moore W, Pflug JM, Archambeault SL, Hoang T, Chen J-Y (2021) Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data. In: Spence J, Casale A, Assmann T, Liebherr JК, Penev L (Eds) Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020). ZooKeys 1044: 41-152. https://doi.org/10.3897/zookeys.1044.62245
Figure 4 Continued.
Data from: Cost effective microsatellite isolation and genotyping by high throughput sequencing
High throughput sequencing (HTS) has emerged as a valuable tool for the rapid isolation of genetic markers for population genetics and pedigree analysis. HTS-based SNP (single nucleotide polymorphism) genotyping protocols like RAD (Restriction-site associated DNA) sequencing or hybrid capture, allow for the isolation of thousands of markers from any non-model organism. However, these protocols are relatively laborious and expensive and the resulting high marker density is not always necessary. Since HTS technology has also greatly simplified the isolation and genotyping process of microsatellite markers, we develop microsatellite markers as a cost efficient and simple alternative to SNP genotyping. We present low coverage genome sequencing data from seven distantly related spider species (Argiope bruennichi, Larinia jeskovi, Oedothorax restusus, Pisaura mirabilis, Australomisidia ergandros, Cheiracanthium punctorium, Theridion grallator) and show the utility of HTS for microsatellite isolation. We also present a simple Illumina amplicon sequencing protocol to genotype microsatellites from multiplex PCR amplicons in the Hawaiian happy face spider T. grallator. We discuss advantages and drawbacks of the use of microsatellites for a range of research questions, and highlight an unexpectedly fast decay and gain of repeat loci for T. grallator.
Data from: Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.
Classically, the mitochondrial genome is sequenced by a series of amplicons using conserved PCR primers. Here we show how shot-gun transcriptome sequencing can be used to obtain the complete set of protein-coding genes from the mtDNA of four passerine bird species. With these sequences, we address the still unresolved basal Passerida relationships (Aves: Passeriformes). Our analysis suggests a new hypothesis for the basal relationships of Passerida, namely a clade grouping Sylvioidea and Passeroidea, with Paridae and Muscicapidae as successive sister groups to this clade. This study demonstrates the usefulness of next-generation sequencing transcriptome sequencing for obtaining new mtDNA genomes.
16S rRNA sequences of gut microbiome and meta data
<p><b>Objective:</b>To understand the role of gut microbiome in influencing the pathogenesis of neuromyelitis optica spectrum disorders (NMOSD)among patients of south Indian origin.</p> <p><b>Methods:</b>In this case control study, stool and blood samples were collected from 39 NMOSD patients, including 17 with aquaporin 4 IgG antibodies (AQP4+) and 36 matched controls. 16S rRNA sequencing was used to investigate the gut microbiome. Peripheral CD4+ T cells were sorted in 12 healthy controls & 12 AQP4+NMOSD patients, RNA extracted, and immune gene expression analyzed using Nanostring nCounter human immunology kit code set.</p> <p><b>Results: </b>Microbiota community structure (beta-diversity) differed between AQP4+ NMOSD and healthy controls (p <0.001, pairwise PERMANOVA test). Linear discriminatory analysis effect size (LEfSe) identified several members of the microbiota that were altered in NMOSD patients, including an increase in <i>Clostridium bolteae </i>(effect size 4.23, pvalue 0.00007). <i>C.bolteae </i>was significantly more prevalent (p=0.02) amongAQP4-IgG + NMOSD (n= 8/17 subjects)compared to seronegative patients (n= 3/22) and was absent among healthy stool samples.<i>C bolteae </i>has a highly conserved glycerol uptake facilitator and related aquaporin protein(p59-71) that shares sequence homology with AQP4 peptide(p92-104), positioned within an immunodominant (AQP4specific)T cell epitope (p91-110).Presence of <i>C. bolteae</i> correlated with expression of inflammatory genes associated with both innate and adaptive immunity and particularly involved in plasma cell differentiation ,B cell chemotaxis and Th17 activation.</p> <p><b>Conclusion: </b>Our study described elevated levels of <i>C. bolteae </i>associated with AQP4+ NMOSD among Indian patients. It is possible that this organism may be causally related to the immunopathogenesis of this disease in susceptible individuals.</p> <p><b>Objective:</b>To understand the role of gut microbiome in influencing the pathogenesis of neuromyelitis optica spectrum disorders (NMOSD)among patients of south Indian origin.</p> <p><b>Methods:</b>In this case control study, stool and blood samples were collected from 39 NMOSD patients, including 17 with aquaporin 4 IgG antibodies (AQP4+) and 36 matched controls. 16S rRNA sequencing was used to investigate the gut microbiome. Peripheral CD4+ T cells were sorted in 12 healthy controls & 12 AQP4+NMOSD patients, RNA extracted, and immune gene expression analyzed using Nanostring nCounter human immunology kit code set.</p> <p><b>Results: </b>Microbiota community structure (beta-diversity) differed between AQP4+ NMOSD and healthy controls (p <0.001, pairwise PERMANOVA test). Linear discriminatory analysis effect size (LEfSe) identified several members of the microbiota that were altered in NMOSD patients, including an increase in <i>Clostridium bolteae </i>(effect size 4.23, pvalue 0.00007). <i>C.bolteae </i>was significantly more prevalent (p=0.02) amongAQP4-IgG + NMOSD (n= 8/17 subjects)compared to seronegative patients (n= 3/22) and was absent among healthy stool samples.<i>C bolteae </i>has a highly conserved glycerol uptake facilitator and related aquaporin protein(p59-71) that shares sequence homology with AQP4 peptide(p92-104), positioned within an immunodominant (AQP4specific)T cell epitope (p91-110).Presence of <i>C. bolteae</i> correlated with expression of inflammatory genes associated with both innate and adaptive immunity and particularly involved in plasma cell differentiation ,B cell chemotaxis and Th17 activation.</p> <p><b>Conclusion: </b>Our study described elevated levels of <i>C. bolteae </i>associated with AQP4+ NMOSD among Indian patients. It is possible that this organism may be causally related to the immunopathogenesis of this disease in susceptible individuals.</p>
Figure 7 from: Jouladeh Roudbar A, Eagderi S, Esmaeili HR, Coad BW, Bogutskaya N (2016) A molecular approach to the genus Alburnoides using COI sequences data set and the description of a new species, A. damghani, from the Damghan River system (the Dasht-e Kavir Basin, Iran) (Actinopterygii, Cyprinidae). ZooKeys 579: 157-181. https://doi.org/10.3897/zookeys.579.7665
Figure 7 - Two views of Cheshmeh Ali, Damghan, type locality of Alburnoides damghani sp. n.
Figure 9 from: Tanaka H, Dung LD, Higashi R, Tsukagoshi A (2016) A new interstitial ostracod species of the genus Paracobanocythere from Vietnam, with mitochondrial CO1 sequence data of three Asian species. ZooKeys 559: 17-33. https://doi.org/10.3897/zookeys.559.6751
Figure 9 - Scatter plots of valves of Paracobanocythere vietnamensis sp. n.
Genome Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs
<p>These are the supplementary files of the article "Genome Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs".</p>
Data from: Direct PCR meets high-throughput sequencing - metabarcoding of chironomid communities without DNA extraction
<p>Abstract</p> <p>Metabarcoding is a valuable tool for investigating insect community compositions. However, high-throughput applications, such as for biomonitoring, require cost-effective and user-friendly procedures. To investigate if the time-consuming and labour-intensive DNA isolation step can be omitted in metabarcoding, we studied the difference in detection rates and individual read abundance using standard DNA isolation versus direct PCR protocols. Metabarcoding with and without DNA isolation was performed on artificially created communities with known composition as well as on natural communities both of the dipteran family Chironomidae to compare detection rates, individual read abundances and presence-absence community composition. The data sets include read abundances of all artificial and natural community samples. Compositions of the samples per data set are described in the respective README files. ASVs/OTUs and their respective DNA sequences are given. R Scripts for bioinformatic processing (dada2 for ASVs, JAMP for OTUs) are provided.</p> <p>Methods</p> <p>Chironomidae were retrieved from artificial ponds of the Eußerthal Ecosystem Research Station (EERES) near Landau, Germany, in 2019 and 2020. Adult specimens were collected from passive emergence traps. Chironomid samples were stored in 70% ethanol and later dried at 60°C. Samples were then finely ground using a bead mill. PCR-grade water was added to each tissue sample and thoroughly vortexed. The tissue-water mixes were frozen at -20°C until further analysis. Artificial communities were created by pipetting tissue-water mixes of individual chironomids. Natural communities from eight ponds and five consecutive sampling dates were selected to assess the applicability of the dPCR approach compared to standard metabarcoding protocols on natural chironomid communities. Four of the artificial ponds were treated with the mosquito control agent <em>Bacillus thuringiensis israelensis</em> (Bti). Tissue-water mixes of artificial and natural communities were both directly applied to PCR and used for DNA isolation. Illumina sequencing was performed and raw data were bioinformatically prepared. For more details see "Direct PCR meets high-throughput sequencing - metabarcoding of chironomid communities without DNA extraction" (Röder & Schwenk 2023). Raw sequences are available through GenBank SRA archive (BioProject accession number PRJNA989176). </p>
RNA Sequencing Analysis in Large Vessel Occlusion Stroke DATA Bank
ClinicalTrials.gov study NCT03490552. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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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.