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21 results for “Ion Torrent”
Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)
<p>Here, we present the Ion Torrent® next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include <em>Galeorhinus galeus</em> (17,487 bp; GenBank accession number ON652874), <em>Mustelus asterias</em> (16,708; ON652873), <em>Mustelus mosis</em> (16,755; ON075077), <em>Mustelus palumbes</em> (16,708; ON075076), and <em>Triakis megalopterus</em> (16,746 bp; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes (<em>tRNA<sup>Leu</sup></em><sup> </sup>and <em>tRNA<sup>Ser</sup> </em>are duplicated), except for <em>G</em>. <em>galeus</em> which contains 23 tRNA genes where <em>tRNA<sup>Thr</sup> </em>is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories.</p>
Ion Torrent data for the genome assembly and phylogenomic placement of mitochondrial genomes with a focus on houndsharks (Chondrichthyes: Triakidae)
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Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing
The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad) and one angiosperm species. We show that these NGS platforms differ in the quantity of returned sequence data, unique microsatellite data and primer design opportunities, mostly consistent with the differences in read length. The strength of the PGM lies in the large amount of data generated at a comparatively lower cost and time. The strength of GS-FLX lies in the return of longer average length sequences and therefore greater flexibility in producing markers with variable product length, due to longer flanking regions, which is ideal for capillary multiplexing. These differences need to be considered when choosing a NGS method for microsatellite discovery. However, the ongoing improvement in read lengths of the NGS platforms will reduce the disadvantage of the current short read lengths, particularly for the PGM platform, allowing greater flexibility in primer design coupled with the power of a larger number of sequences.
Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with insufficient taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.
Data from: Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform
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Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
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Data from: Microsatellite marker development by multiplex Ion Torrent PGM sequencing: a case study of the endangered Odorrana narina complex of frogs
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Data from: Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing
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Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing
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Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?
A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.
Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?
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Data from: Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology
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Transcriptome profiling of single HEK293 cells with UMIs on Ion Torrent Proton (Run 20160225)
GEO Series GSE89235. Homo sapiens. 76 samples. Type: Expression profiling by high throughput sequencing.
Ion Torrent RNA-sequencing of exosomes isolated from ovarian cancer cells, fibroblasts and adipocytes
GEO Series GSE77318. Homo sapiens. 13 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Transcriptome profiling of single HEK293 cells with UMIs sequenced on Ion Torrent Proton (Run 20151215)
GEO Series GSE79130. Homo sapiens. 47 samples. Type: Expression profiling by high throughput sequencing.
A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
GEO Series GSE98562. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Extraskeletal Osteosarcoma Harboring ETV6:NTRK3 Fusion Treated Successfully with Larotrectinib: A Case study [Ion Torrent Oncomine Comprehensive Assay Plus]
GEO Series GSE308605. Homo sapiens. 1 samples. Type: Other.
Mapping replication domains using the Ion Torrent semiconductor sequencing platform [BrdU-IP]
GEO Series GSE115847. Mus musculus. 2 samples. Type: Other.
Transcriptome profiling of single HEK293 cells with UMIs on Ion Torrent Proton (Run 20150702)
GEO Series GSE89234. Homo sapiens. 38 samples. Type: Expression profiling by high throughput sequencing.
The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [Ion Torrent Proton]
GEO Series GSE48034. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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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.