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19,342 results for “Sequences”
Fig 4 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China
Fig 4. Genome map of Sphingobacterium deserti sp. nov. ZWT. Concentric tracks from the inside to the outside represent the GC nucleotide bias; the GC content; tRNA and rRNA genes on the reverse strand; tRNA and rRNA genes on the forward-strand; reverse-strand coding sequences (CDSs); and forwardstrand CDSs. doi:10.1371/journal. pone.0122254.g004
Fig 1 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China
Fig 1. Electron micrograph of the cell morphology of strain ZWT. doi:10.1371/journal.pone.0122254.g001
16S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p><strong>Metabarcoding - 16S ASV generation and taxonomic assignment</strong>. Raw 16S paired-end sequences were subjected to a data quality control step and subsequently imported into the QIIME2 pipeline v.2022.2.0. Leftover primers and adapter sequences were removed through cutadapt. The amplicon sequence variants (ASV) table, which represent true biological sequences within each sample, was generated using the denoised-paired method including truncation, denoising, dereplication, merging, and chimera filtering of the DADA2 (Divisive Amplicon Denoising Algorithm 2) plugin inside QIIME2. Default parameters were used with the exception of the forward and reverse sequence length (--p-trunc-len-f and --p-trunc-len-r), that were set to 220 and 180, respectively. Processed reads that passed all these filters were used for taxonomy classification. The V4-V5 regions were extracted from the pre-formatted reference sequences and taxonomy file built on the SILVA 138 99% OTUs database and the vsearch v.2.6.2 global alignment implemented in QIIME2 was used.</p>
Fig 5 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China
Fig 5. Whole-genome optical mapping barcode of Sphingobacterium deserti sp. nov. ZWT. Vertical lines represent restriction sites; distances between lines represent fragment sizes.
Bacterial cell surface characterization by phage display coupled to high-throughput sequencing
<p>This record contains the processed high-throughput sequencing data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing." Data was generated using the <a href="https://github.com/caseygrun/phage-seq">Snakemake workflows and Jupyter notebooks in this repository</a> and is intended to be analyzed further using the notebooks in that repository</p> <p>Each tarball within this record, when expanded, populates the <code>results</code> and <code>intermediate</code> directories of one of those workflows: <code>alpaca-library</code> ,<code>panning-small</code>, <code>panning-massive</code>, or <code>panning-extended</code>. Clone the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>, then download one or more of these tarballs to the corresponding directory of that directory. For example:</p> <blockquote> <pre><code>git clone https://github.com/caseygrun/phage-seq.git cd panning-extended wget https://zenodo.org/records/11246658/files/panning-extended-results.tar.gz tar vzxf panning-extended-results.tar.gz</code></pre> </blockquote> <p>More detailed instructions are included in the README for the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>.</p>
Dataset microbial counts and sequencing of BSF larvae to assess vertical transmission of E. coli
<p>Sequencing data available from <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1068952" target="_blank" rel="noopener">BioProject PRJNA1068952</a></p>
Dataset qPCR and sequencing of BSF larvae gut regions
<p>Sequencing data available from <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA706185/" target="_blank" rel="noopener">BioProject PRJNA706185</a></p>
U-Pb-Th SHRIMP & LA-ICP-MS complementary data of "The bimodal Fii-A2-type and calc-alkaline volcanic sequence of the Aljustrel brownfield region, Iberian Pyrite Belt, SW Iberian Massif"
<p>U-Pb-Th complementary data of "The bimodal Fii-A2-type and calc-alkaline volcanic sequence of the Aljustrel brownfield region, Iberian Pyrite Belt, SW Iberian Massif" <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.chemer.2023.126049" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.chemer.2023.126049</span></span></a></p>
Melanoma Cell Lines SLC22A17 Bisulfite Sequencing Raw Data
<p>Bisulfite sequencing raw data of SLC22A17 gene obtained in melanoma cell lines. The data will be published in the article entitled "<span>Identification of <em>SLC22A17</em> DNA methylation hotspot as a potential biomarker in cutaneous melanoma</span>" submitted to Journal of Translational Medicine</p>
Comprehensive survey of common bean viruses in Tanzania using next generation and Sanger sequencing techniques
<p>Common bean (<em>Phaseolus vulgaris</em> L.) is an important legume crop in Tanzania and elsewhere in the tropics and subtropics. We employed a next-generation sequencing technique to detect viruses in common bean plant samples collected from five agricultural research zones in the country. The aim was to target and sequence virus-derived small RNAs. To achieve this, total RNA was isolated from dry leaf samples using the CTAB method. The CTAB buffer contained 2% CTAB, 100 mM Tris–HCl, 20 mM EDTA, 2.5 M NaCl, freshly prepared 1% sodium sulfite, 2% PVP and 2.5% 2-mercaptoethanol in nuclease-free water. Total RNA was sent to Fasteris in Switzerland where the small RNA was purified by electrophoresis in an acrylamide gel. The small RNA library was prepared using the Illumina TrueSeq small RNA sample preparation kit (Illumina Inc., San Diego, CA, USA). Viruses were detected using VirusDetect software (v.1.6 and v.1.7) (available at http://bioinfo.bti.cornell.edu/cgi-bin/virusdetect/index.cgi) and supercomputer at CSC.fi. Viruses detected belonged to at least 11 genera.</p>
The molecular investigation of Blood cockles (Anadara granosa) associated bacterial communities using 16S rRNA sequencing
<p>This data on the bacterial communities and its diversity associated with <em>Anadara granosa</em>. The <em>Anadara granosa</em> samples were obtained from two major estuaries in Penang, Malaysia using a culture dependent and 16S rRNA sequencing approach.</p>
Plasmid sequences for the paper "A FRET based biosensor for measuring Gα13 activation in single cells"
<p>Plasmid sequences for the paper "A FRET based biosensor for measuring Gα13 activation in single cells"</p>
FIGURE 20. Phylogenetic relationship among selected Dryocosmus and Chilaspis species based COI sequences resolved using with MrBayes 3.2.6 in Discovery of a new species of Dryocosmus Giraud, 1859 (Hymenoptera: Cynipidae: Cynipini) on Castanopsis tibetana from China
FIGURE 20. Phylogenetic relationship among selected Dryocosmus and Chilaspis species based COI sequences resolved using with MrBayes 3.2.6 (Ronquist et al. 2012). Two independent MCMC runs were run with the following parameters: 10 million gens, nst = 6, rates = gamma, sample frequency = 1/1,000, burn-in = 30%, and otherwise default. The length of the branches is drawn to scale of genetic distance and the number over branches is posterior probability. (Generic name abbreviations: A. = Andricus, Ch. = Chilaspis, D. = Dryocosmus)
Supplementary material 1 from: Binh HT, Ngoc NV, Tagane S, Toyama H, Mase K, Mitsuyuki C, Strijk JS, Suyama Y, Yahara T (2018) A taxonomic study of Quercus langbianensis complex based on morphology, and DNA barcodes of classic and next generation sequences. PhytoKeys 95: 37-70. https://doi.org/10.3897/phytokeys.95.21126
Figure S1, S2 : Explanation note: Figure S1. Bayesian phylogeny of 29 samples of Quercus and one Trigonobalanus (outgroup) based on ITS sequences. Branches are labeled with posterior probabilites. Figure S2. Bayesian phylogeny of 29 samples of Quercus and one Trigonobalanus (outgroup) based on concatenated rbcL and matK sequences. Branches are labeled with posterior probabilities.
Supplementary material 9 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
Bland-Altman plots for the total fish eDNA (a), Japanese anchovy (Engraulis japonicus; b) and Japanese jack mackerel (Trachurus japonicus; c). Dashed lines indicate 95% uppper and lower limits and solid line indicates mean value.
Supplementary material 6 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The numbers of eDNA copies of marine fish species quantified by metabarcoding with the internal standard DNA
Supplementary material 8 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between MiSeq sequence reads and DNA copy numbers quantified by qPCR. Correlations for the total fish eDNA (all data, a; enlarged figure, b), Japanese anchovy (Engraulis japonicus; all data, c; enlarged figure, d) and Japanese jack mackerel (Trachurus japonicus; all data, e; enlarged figure, f). Dashed and soild lines indicate 1:1 line and linear regression line, respectively. Regression lines in the enlarged figures were drawn by excluding outliers. All regression lines, except for the lines for total fish eDNA, were significant (P < 0.05). Dotted boxed regions in a, c and e correspond to the range of the graphs in b, d and f, respectively. The intensity of red colour indicates the slope of the regression line used to convert sequence reads to the copy numbers.
Supplementary material 4 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between MiSeq sequence reads and copy numbers of standard DNAs for 52 samples. Blue line indicates the linear regression between sequence reads and copy numbers. The regression lines are used to convert the MiSeq reads into the calculated copy numbers. Numbers in a grey region indicate sampling date. Note that regression slopes are different amongst samples, i.e. the number of sequence reads generated per eDNA copy is different amongst samples.
Supplementary material 5 from: Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding and Metagenomics 2: e23297. https://doi.org/10.3897/mbmg.2.23297
The relationship between regression residuals and copy numbers of standard DNAs for 52 samples. Dashed line indicates zero residuals.
Supplementary material 1 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937
Data Table. Taxon sample and UCE sequencing results : Explanation note: Samples highlighted in red were sequenced for Starrett et al. (2017).
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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)
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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.