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718 results for “illumina”
Data from: The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio
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Data from: Genome-wide insights into population structure and genetic history of Tunisian local cattle using the Illumina BovineSNP50 Beadchip
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Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex
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Data from: Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)
Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5' end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (eight forward primers + 12 reverse primers yield 8 x 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy.
Data from: Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species
The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short-read sequence data and our assembly in recovering this gene family. We highlight the benefits and shortcomings of these methods. Compared with data generated from traditional polymerase chain reaction, cloning and Sanger sequencing methodologies, sequence data generated using our pipeline increases yield and sequencing efficiency without reducing the number of unique genes amplified. A cloning step is not required, therefore shortening data generation time. The novel downstream methodologies and workflows described provide a tool to be utilized by many fields of biology, to access and analyze the vast quantities of data generated. By combining laboratory and in silico methods, we provide a means of extracting genomic information for multigene families without complete genome sequencing.
Data from: Characterization of 42 polymorphic microsatellite loci in Mimulus ringens (Phrymaceae) using Illumina sequencing
Premise of the study: Microsatellite markers were isolated and characterized in Mimulus ringens (Phrymaceae), a herbaceous wetland perennial, to facilitate studies of mating patterns and population genetic structure. Methods and Results: A total of 42 polymorphic loci were identified from a sample of 24 individuals from a single popula- tion in Ohio, USA. The number of alleles per locus ranged from two to nine, and median observed heterozygosity was 0.435. Conclusions: This large number of polymorphic loci will enable researchers to quantify male fitness, patterns of multiple pa- ternity, selfing, and biparental inbreeding in large natural populations of this species. These markers will also permit detailed study of fine-scale patterns of genetic structure.
Data from: Successful recovery of nuclear protein-coding genes from small insects in museums using illumina sequencing
In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.
illumina Hi-seq
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M-values from Illumina EPIC BeadChip DNA methylation analyses on DNA in whole blood for children exposed to PFAS
<p>Perfluoroalkyl substances (PFASs) are widespread synthetic substances with various adverse health effects. A potential mechanism of toxicity for PFASs is via epigenetic changes, such as DNA methylation. In this exploratory study with school-age children exposed to PFASs through drinking water highly contaminated from firefighting foams, we aimed to investigate whether exposure to PFASs was associated with alteration in DNA methylation and epigenetic age acceleration. Sixty-three children aged 7–11 years from the Ronneby Biomarker Cohort (Sweden) were included. The children were either controls with only background exposure (n=32; perfluorooctane sulfonic acid: median 2.8 and range AQ11 1–5ng/ml) or those exposed to very high levels of PFASs (n=31; perfluorooctane sulfonic acid: median 295 and range 190–464ng/ml). These two groups were matched on sex, age, and body mass index. Genome-wide methylation of whole-blood DNA was analyzed using the Infinium MethylationEPIC BeadChip kit.</p>
Data from: Characterization of microsatellite loci for the Gulf Coast waterdog (Necturus beyeri) using paired-end Illumina shotgun sequencing and cross-amplification in other Necturus
[No abstract filled]
Illumina Inifinium HumanMethylation450 array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment
<p>The current data sets represent the raw methylated (M) and unmethylated (U) intensities on 38 paired samples, with cancer (non-metastatic colorectal cancer) and healthy (normal mucosa) tissue available for each single sample. The data were obtained in the context of the ongoing population-based case-control study DACHS (<em>Darmkrebs: Chancen der Verhuetung durch Screening</em>, <a href="http://dachs.dkfz.org/dachs/">http://dachs.dkfz.org/dachs/</a>), extensively described in Brenner et al. (2011). Data collecting and patient recruitment procedures as well as the processes of DNA isolation and methylation profiling using the Infinium HumanMethylation450 BeadChip array (Illumina) are similar to those described in Gündert et al. (2017).</p> <p>In the context of our experiment, all 38 samples were handled by means of paired bisulfite (BS) and oxidative bisulfite (oxBS) procedures. The reason for such paired treatment is the fact that the BS procedure, commonly used for derivation of the M and U intensities, can only differentiate between methylated and unmethylated cytosine bases, and cannot discriminate between 5mC and 5hmC. In order to determine the level of 5hmC at a considered nucleotide position that is indispensable for our analyses of the 5hmC measures, the oxBS procedure was applied. The name of the applied procedure (BS or oxBS) as well as the name of the corresponding intensities (M or U) can be read off from the name of the corresponding file. Each file contains 77 columns. The first column provides the designation of the corresponding CpG, the remaining 76 columns provide the corresponding intensities on healthy and cancer tissue, in alternating order.</p> <p>References:</p> <p>Brenner H, Chang-Claude J, Seiler CM et al. Protection from colorectal cancer after colonoscopy: a population-based, case-control study. Ann Intern Med 2011; 154: 22-30.</p> <p>Gündert M, Edelmann D, Benner A, et al. Genome-wide DNA methylation analysis reveals a prognostic classifier for non-metastatic colorectal cancer (ProMCol classifier). Gut 2017; 1-10.</p>
Illumina data, assemblies and Rfam annotations for Station036_2207
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Data from: Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus
The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that: i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod endosymbiont studies.
Illumina microarray data for our protocol
<p>Illumina microarray data for our protocol</p>
Supporting data for Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater
<p>This dataset contains the FASTQ files used in the paper <em>Comparison of Oxford Nanopore and Illumina sequencing for SARS-CoV-2 variant monitoring in wastewater</em>. </p> <p>The FASTQ files are classified in 2 different folders: MinION and MiSeq. Inside the MinION folder, there are two more folders, one for the R9.4.1 flow cell data and the other for the R10.4.1 flow cell data. </p> <p>Twist synthetic RNA mixtures are named as mix1, mix2, etc. </p> <p>Twist synthetic RNA corresponding to the Wuhan sequence is named as mix11_WH</p> <p>Wastewater samples are named as WWTP_1, WWTP_2, etc. </p>
Double digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles
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Data from: Using Illumina Next Generation Sequencing Technologies to sequence multigene families in de novo species
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Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community
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Data from: Improving Illumina assemblies with Hi-C and long reads: an example with the North African dromedary
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Data from: Characterization of 42 polymorphic microsatellite loci in Mimulus ringens (Phrymaceae) using Illumina sequencing
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.