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19,342 results for “sequence”
Draft genome assemblies of killifish from the Fundulus genus with ONT and Illumina sequencing platforms
<p>Four species from the genus Fundulus were selected for genome sequencing to study the physiological and genetic mechanisms that diverge between euryhaline and stenohaline freshwater species within this cyprinodontiform order of ray-finned fishes.</p>
Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos
<p><strong>Content</strong></p> <p>This dataset contains 15 2D time-lapse fluorescence microscopy image sequences recorded with confocal laser-scanning microscopy. Each movie shows an epithelial tissue laser nanoablation experiment conducted in a Drosophila embryo.</p> <p>For each sequence, the dataset contains kymographs (one-dimensional space-time plots) of a supracellular cable that is cut during the ablation, and manually created tracks of visible features, such as the resulting cut ends. These tracks allow to estimate, for instance, recoil velocities of the cut tissue and may be used to evaluate automated methods for estimating said velocities.</p> <p>This dataset is used in the manuscript to evaluate various variational approaches for joint motion estimation and source identification:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations. 2019.</p> <p><strong>Description</strong></p> <p>The movies depict a square region of approximately <span class="math-tex">\(42.2 \times 42.2 \, \mathrm{\mu m}^{2}\)</span> at a spatial resolution of <span class="math-tex">\(250 \times 250\)</span> pixels. A typical sequence contains between 60 and 100 frames. They temporal interval between recorded frames was <span class="math-tex">\(727.67 \, \mathrm{ms}\)</span>.</p> <p>Each sequence features cell membranes labelled with E-cadherin:GFP and shows a single plasma-induced laser nanoablation. The destructed tissue region is roughly of <span class="math-tex">\(2 \, \mathrm{\mu m}\)</span> length. This ablation is expected to have a width of the order of the size of one pixel. During the ablation the acquisition is paused, resulting in a black image.</p> <p>For the used microscopy techniques and for the preparation of flies, as well as for the details of the laser ablation method, see the paper:</p> <p>E. Scarpa, C. Finet, G. B. Blanchard, and B. Sanson. Actomyosin-driven tension at compartmental boundaries orients cell division independently of cell geometry In Vivo. Dev. Cell, 47(6):727–740.e6, December 2018. URL: <a href="https://doi.org/10.1016/j.devcel.2018.10.029">https://doi.org/10.1016/j.devcel.2018.10.029</a></p> <p>The kymographs and the manually created annotations (tracks) of features were created using Fiji (<a href="https://fiji.sc/">https://fiji.sc/</a>).</p> <p><strong>Content</strong></p> <p>The dataset contains 15 sequences placed in the following folder structure:</p> <ul> <li>SqAX3_SqhGFP42_GAP43_TM6B <ul> <li>190216E4PSB1</li> <li>190216E5PSB1</li> <li>190216E5PSB2</li> <li>190216E6PSB1</li> <li>190216E8PSB1</li> <li>E2PSB1</li> <li>E5PSB2</li> <li>E8PSB1</li> <li>PSB1E1</li> <li>PSB4</li> </ul> </li> <li>SqhGFP40 <ul> <li>e1_PSB8</li> <li>e3_PSB9</li> <li>e3_PSB10</li> <li>e4_PSB11</li> <li>e4_PSB12</li> </ul> </li> </ul> <p>Each folder contains:</p> <ul> <li>The sequence itself in TIF format, e.g. "190216E4PSB1PMT - PMT [560-] _C1.ome.tif".</li> <li>A file "reslice.roi" that indicates the location/direction of the cut supracellular cable.</li> <li>3 different kymographs for each sequence obtained by taking avg/max/sum projections in Fiji orthogonal to the line specified in "reslice.roi", e.g. <ul> <li>"AVG_Reslice of 190216E4PSB1PMT.tif",</li> <li>"MAX_Reslice of 190216E4PSB1PMT.tif",</li> <li>"SUM_Reslice of 190216E4PSB1PMT.tif".</li> </ul> </li> <li>Text files that state the time/space coordinates of manually tracked features in the kymographs, e.g. <ul> <li>"cutend_L.txt" (coordinates of the left cut end after the ablation),</li> <li>"cutend_R.txt" (coordiantes of the right cut end),</li> <li>"feat_X.txt" (coordinates of additional features, where X is a number and L or R).</li> </ul> </li> <li>A ZIP file "manual_ROIs.zip" that contains all the coordinates of tracked features of the kymograph in ROI format (e.g. "cutend_L.roi").</li> </ul> <p><strong>Usage</strong></p> <p>The sequences, kymographs, and the tracks can be viewed using, for example, Fiji.</p> <p>For the automated analysis, see the Python code that accompanies the manuscript above. It is available at https://dx.doi.org/XXX</p> <p><strong>License information</strong></p> <p>This dataset is released under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. See <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NA-SC 4.0</a>.</p> <p><strong>How to cite this dataset</strong></p> <p>If you use this dataset in an academic publication, please consider citing the paper:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. Joint Motion Estimation and Source Identification using Convective Regularisation with an Application to the Analysis of Laser Nanoablations. 2019.</p> <p>To cite solely the dataset, please use:</p> <p>L. F. Lang, N. Dutta, E. Scarpa, B. Sanson, C.-B. Schönlieb, and J. Étienne. (2019). Microscopy image sequences and annotated kymographs of laser ablation experiments in Drosophila embryos [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.3257654">http://doi.org/10.5281/zenodo.3257654</a></p>
Supplementary data for: Detection of expressed mutations in acute myeloid leukemia cells using single cell RNA-sequencing
<p>Supplemental data for the publication:<br> Detection of expressed mutations in acute myeloid leukemia cells using single cell RNA-sequencing </p> <p>Contents: <br> - expression_matrices.tar - Gene/Barcode expression matrices from `cellranger count`<br> - *.seurat.rds - R object files with Seurat analyses and data structures for each sample<br> - scrna_mutations.tar.gz - copy of a git repository containing additional scripts and data - also hosted at <a href="https://github.com/genome/scrna_mutations">https://github.com/genome/scrna_mutations</a> (snapshot as of May 20, 2019)</p>
A comparison of automatic cell identification methods for single-cell RNA-sequencing data
<p>Benchmark datasets used to evaluate the performance of 22 classifiers for cell type classification for scRNA-seq data</p>
Bigwig files of ChIP and RNA sequencing experiments in Theileria annulata
<p>This repository provides bigwig files for ChIP and RNA sequencing experiments in Theileria annulata. DeepTools generated Coverage files, ReadCount normalised files and SES normalised files are provided. Also provided are genome and annotation files for visualisation with IGV software.</p>
The Caedibacter taeniospiralis genome sequence and annotation
<p>Interest in host-symbiont interactions is continuously increasing, not only due to the relevance and<br> prevalence of microbiomes. Started with the detection and description of novel symbionts, attention<br> moves to the molecular consequences and innovations of symbioses. However, molecular analysis requires<br> genome data which is dicult to obtain from obligate intracellular and uncultivated bacteria.We describe<br> here the Caedibacter taeniospiralis genome and transcriptome, identified by DNA and RNA Dual-Seq<br> of infected paramecia.</p> <p>Data inlcudes a genome FASTA file, annotations of genes and operons in gff format, and the compelte annotation in Geneious format.</p>
DNA sequences alignements for 27 species of ticks (SCO50 matrix)
<p>The two files contain respectively the concatenation of DNA sequences alignements for 27 species of ticks (SCO50 matrix, n=952 genes) and to the partition file indicating the positions of each gene in the concatenation.</p> <p>The data set corresponds to the article "A transcriptome-based phylogenetic study of hard ticks (Ixodidae)" to be published in Scientific Reports, by N Pierre Charrier, Axelle Hermouet, Caroline Hervet, Albert Agoulon,<br> Stephen Barker, Dieter Heylen, Céline Toty, Karen McCoy, Olivier Plantard, Claude Rispe.</p>
HiPR-FISH PacBio Sequencing Data
<p>This dataset contains raw fastq files from PacBio sequencing for HiPR-FISH experiments.</p>
MinION sequence data: MinION sequencing of colorectal cancer tumor microbiomes – a comparison with amplicon-based and RNA-Sequencing
<p>MinION sequencing data that was unmapped by minimap2 for the 11 samples using in the "MinION sequencing of colorectal cancer tumor microbiomes – a comparison with amplicon-based and RNA-Sequencing" paper.</p>
Bayesian network analysis of plasma microRNA sequencing data in patients with venous thrombosis
<p>This dataset contains the results of 2 related analyses, described in "Bayesian network analysis of plasma microRNA sequencing data in patients with venous thrombosis" (European Heart Journal Supplements, OUP). Link to the article: https://www.hal.inserm.fr/inserm-02310241</p> <p>1) In the directory "miRNAs_MARTHA_GWAS" : GWAS summary statistics for 162 circulating miRNAs in 344 VTE patients from the MARTHA cohort.</p> <p>Header for each summary file:</p> <p>Trait: miRNA id<br> chr: Chromosome<br> pos.hg19: Position of the variant in hg19/GRCh37 coordinates<br> SNP: rsid<br> A1: Reference allele on the forward strand<br> A2: Alternate allele on the forward strand<br> freq_A1: Frequency of reference allele<br> rsqr: Imputation quality defined by MACH<br> beta_A1: Estimated effect size (beta regression coefficient) of reference allele<br> se_A1: Estimated standard error of beta<br> p: p-value (significance of estimated beta)<br> z.score: Z-score</p> <p> </p> <p>2) In the directory "meta_analysis": Random effect meta-analysis combining the results of our GWAS on the MARTHA cohort, and the results from a similar analysis conducted by Nikpay et al. (doi: 10.1093/cvr/cvz030). Summary statistics of 142 microRNAs, common to both datasets, were processed (and combine 1054 samples).</p> <p>Header for each summary file:</p> <p>chr: Chromosome<br> pos.hg19: Position of the variant in hg19/GRCh37 coordinates<br> SNP: rsid<br> A1: Reference allele on the forward strand<br> A2: Alternate allele on the forward strand<br> N: Sample size<br> Q: Cochran's heterogeneity statistic<br> Q.p: p-value of Cochran's Q<br> beta_A1: Estimated effect size (beta regression coefficient) of reference allele<br> se_A1: Estimated standard error of beta<br> p: p-value (significance of estimated beta)</p> <p> </p>
Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations
<p>Scripts and derived data for the indicated paper. Links to the <a href="https://zenodo.org/record/1204695">original data</a> and <a href="https://zenodo.org/record/3497585">library source code</a> used to generate this material. Inflate the ENU_mutation_classification.tar.gz archive, remove the ENU_mutation_classification/classifier directory (this will be replaced). Move all others archives into the ENU_mutation_classification directory and inflate them.</p>
example stimuli of "Behavioral effects of rhythm, carrier frequency and temporal cueing on the perception of sound sequences"
<p>Exemplary subset of stimuli accompanying the manuscript "Behavioral effects of rhythm, carrier frequency and temporal cueing on the perception of sound sequences"</p>
The Stratigraphic Sequence at Chachondi (CHD02), Section 1
<p>This dataset comprises the details of stratigraphic sequence visible in exposed section at archaeological site of Chachondi (CHD02), discovered in 2015 during explorations carried out by the INHCRF.</p>
Figure 3 in Analysis of mitochondrial cytochrome b gene sequences of marine leech, Pterobdella arugamensis
Figure 3. Haplotype network of P. arugamensis CYTB gene sequences. Different colours represent different locations. The circle size is proportional to the sample number. Each dash on the line symbolises one mutational event. Tiny white circle indicates median vector.
Figure 2 in Analysis of mitochondrial cytochrome b gene sequences of marine leech, Pterobdella arugamensis
Figure 2. Representative maximum-likelihood tree showing nine haplotypes of P. arugamensis based on CYTB gene sequences. Ozobranchus jantseanus and Erpobdella japonica from the GenBank database were used as outgroups. The bootstrap percentages (1000 replicates) for maximum likelihood/maximum parsimony/neighbour joining trees are shown.
Figure 1 in Analysis of mitochondrial cytochrome b gene sequences of marine leech, Pterobdella arugamensis
Figure 1. Locations of P. arugamensis used in this study. Sampling locations are shown by blue circles: Brunei (TP: Tanjong Pelumpong, PK: Pulau Kaingaran), Surabaya in Indonesia (EJ), and Lombok in Indonesia (EL). Red circle indicates the GenBank sample from Hainan, China. The map was adapted from the USGS National Map Viewer (open access) at http://viewer.nationalmap.gov/viewer/.
Fig. 1 in Phylogenetic Analyses on the Tintinnid Ciliates (Protozoa, Ciliophora) Based on Multigene Sequence Data
Fig. 1. Alignment of the ITS1-5.8S-ITS2 regions from ten reference tintinnid species: Tintinnopsis sp. 1, Tintinnopsis sp. 2, Tintinnopsis sp. 3, T. cylindrica, T. tubulosoides, T. lohmanni, Stenosemella nivalis, Codonellopsis nipponica, Favella campanula, F. taraikaensis, F. ehrenbergii, Metacylis angulata, Eutintinnus pectinis, and Amphorellopsis acuta. Agreement with other sequences is indicated by periods and disagreement by a nucleotide at a position. Gaps introduced to improve the alignment are indicated by dashes. The insertion in ITS1 of F. campanula is labeled. The ITS1 and ITS2 region sequences are shaded; the 5.8S gene sequence is unshaded.
Figs 3–5 in Phylogenetic Analyses on the Tintinnid Ciliates (Protozoa, Ciliophora) Based on Multigene Sequence Data
Figs 3–5. Phylogenetic analyses and photomicrographs in this work. 3, 4 – phylogenetic analyses inferred by ML of internal transcribed spacer (ITS) and 5.8S region sequences and small subunit rDNA sequences. Topologies of trees constructed with other methods (BI, MP, or NJ) were essentially identical, lacking only a few nodes indicated by asterisks in the support values. Posterior probability values for branches of the ML tree and bootstrap values for ML, NJ, and MP trees, respectively, are given on nodes. Newly sequenced species are highlighted in bold. Scale bar in 3 corresponds to 10 substitutions per 100 nucleotide positions, scale bar in 4 corresponds to 5 substitutions per 100 nucleotide positions. 5 – photomicrographs of nine of the 10 newly sequenced tintinnid species in vivo: A – Amphorellopsis acuta; B – Favella taraikaensis; C – F. campanula; D – Tintinnopsis sp. 2; E – Stenosemella nivalis; F – Codonellopsis nipponica; G – Tintinnopsis sp. 3; H – T. lohmanni and I – T. cylindrica. Scale bars: 25 μm.
Figure 3 in Diceratocephala boschmai (Platyhelminthes: Temnocephalida) from crayfish farms in Thailand: investigation of the topographic surface and analysis of 18S ribosomal DNA sequences
Figure 3. The neighbor-joining phylogenetic tree based on the 18S rDNA gene, showing the relationships of D. boschmai with 29 other turbellarian species.
Figure 2 in Diceratocephala boschmai (Platyhelminthes: Temnocephalida) from crayfish farms in Thailand: investigation of the topographic surface and analysis of 18S ribosomal DNA sequences
Figure 2. Surface topography of D. boschmai. A–C) Unhatched and hatched eggs; D) ventral view of a specimen; E) mouth with protruding pharynx; F) thread-like filaments adhered to the pharynx; G, H) a higher magnification of write-dot boxes in 2E; I, J) a higher magnification of write-dot boxes in 2D; K) ventral view of a specimen at posterior end; L) dorsal view of a specimen; M) a higher magnification of write-dot box in Figure L. ad, adhesive disc; af, adhered filaments; ci, ciliated cell; ds, double spines; fi, filament; gr, groove; gv, gravel-like units; in, intertentacular flange; mo, mouth; op, opercular plate; pe, peduncle; pi, pit; sp, single spine; tb, trabecular meshwork; tc, tentacle; th, thread-like filaments; tr, trunk; vi, villi..
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.