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19,342 results for “Sequences”
High frequency of X4/DM-tropic viruses in PBMC samples from HIV-1 recently infected blood donors by massively parallel sequencing: the REDS II Study
<p>Here is a sub-library of the <em>env</em> V3 massively parallel sequencing proviral data generated (by Illumina MiSeq platform) during the early phase of HIV-1 infection in a group of first-time blood donors. Only paired-end reads that encompass the complete V3 region from each dataset were extracted, uploaded and considered for the analysis to avoid artificial generation of <em>in silico</em> chimeras through assembly and to evade inflating the diversity estimates of the V3 region</p>
A Bayesian Approach to Detect Pedestrian Destination-Sequences from WiFi Signatures: Data (tech. report 2013)
<p>This dataset contains the data used in:</p> <p>Danalet, A., Farooq, B. and Bierlaire, M. (2013). A Bayesian Approach to Detect Pedestrian Destination-Sequences from WiFi Signatures, Technical report, Transport and Mobility Laboratory, ENAC, Ecole Polytechnique Fédérale de Lausanne, Lausanne. URL: http://infoscience.epfl.ch/record/189759 (full text available)</p> <p>It contains data and a technical report describing</p> <ul> <li>WiFi traces</li> <li>Pedestrian Semantically-Enriched Routing Graph (SERG), and</li> <li>Potential Attractivity measure (PAM).</li> </ul>
Neutralization Data and Aligned ENV Sequences for Predicting Antibody Affinities using Artificial Neural Networks
<p>Sample file with neutralization data (IC<sub>50</sub>) for different antibodies and viral strains, adapted from J. Huang, G. Ofek, L. Laub, M. K. Louder, N. A. Doria-Rose, N. S. Longo, H. Imamichi, R. T. Bailer, B. Chakrabarti, S. K. Sharma, S. M. Alam, T. Wang, Y. Yang, B. Zhang, S. A. Migueles, R. Wyatt, B. F. Haynes, P. D. Kwong, J. R. Mascola, and M. Connors, “Broad and potent neutralization of HIV-1 by a gp41-specific human antibody.,” <em>Nature</em>, vol. 491, no. 7424, pp. 406–12, Nov. 2012.</p> <p> </p> <p>Aligned ENV sequences downloaded from the HIV Sequence Database (www.hiv.lanl.gov/content/sequence/HIV/mainpage.html). There are 4907 sequences and the alignment length is 1369.</p>
Registration of multi-view echocardiography sequences using a subspace similarity measure
<p>Data employed for the validation of the PCA-based similarity metric proposed in "<em>Registration of multi-view echocardiography sequences using a subspace similarity measure.</em>" Peressutti <em>et al.</em> (under review).</p> <p>Data consists of echocardiography sequences of the Left ventricle of four volunteers (vol_A-vol_D) from different acoustic windows (aw_1-aw_5). The image format is metadata.<br /> For each subject, the ground-truth rigid transformations that aligns each sequence to all the others is provided. Such transformations are provided by optically tracking the position of the ultrasound imaging probe. </p> <p>For more detailed information regarding the datasets, please refer to the paper.</p> <p>Python code for testing the proposed method can be downloaded from (https://github.com/devisperessutti/Python.git), while MATLAB code can be downloaded from (https://github.com/gomezalberto/Matlab.git).</p>
Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing
<p>Analysis scripts and raw data for manuscript titled: "<em>Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing</em>" </p>
A rapid and versatile tool for HIV-1 Drug Resistance Genotyping by Deep Sequencing: supporting dataset
<p>See file `viral_mixes.md` and [manuscript](http://www.sciencedirect.com/science/article/pii/S0166093416301987).</p> <div class="grammarly-disable-indicator"> </div> <div class="grammarly-disable-indicator"> </div>
Ultra-deep sequencing of HIV-1 near full-length and partial proviral genomes reveals high genetic diversity among Brazilian blood donors
<p>Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (São Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70).</p>
C1 CAGE preview sequence run 150519_M00528_0125_000000000-ACUAB
<p>Sequence data (Illumina MiSeq run 150519_M00528_0125_000000000-ACUAB) for the public preview of the C1 CAGE technology.</p>
The free-breathing motion-corrected phase sensitive inversion recovery sequence provides improved myocardial fibrosis evaluation while significantly shortening acquisition time upon comparison to conventional gradient echo sequences: a tripartite comparison of phase-sensitive inversion recovery sequences.
<p>This article includes original research performed at a US Academic Center related to comparison of three separate Phase-Sensitive Inversion Recovery (PSIR) pulse sequences (Breath-hold Single-Shot SFFP, Breath-hold TurboFLASH, and Free-breathing Motion-Corrected SSFP) evaluating the ability of each PSIR sequence to demonstrate myocardial hyperenhancement. All three PSIR sequences were performed as a part of a cardiac MRI performed on a patient clinically referred for cardiac MRI with and without contrast. A total of 28 patients were examined with the three PSIR sequences. All three PSIR sequences were performed in the short axis 10 – 25 minutes after intravenous injection of a Gadolinium-based contrast agent. </p> <p>Evaluation of the PSIR sequences ability to detect myocardial late gadolinium enhancement (LGE) was performed by a retrospective review by two blinded, experienced cardiovascular imagers. The review was a qualitative inspection that included grading by a 5-point Likert scale for the sequence’s ability to resist motion artifact, image resolution, ability to visualize hyperenhancement, and overall satisfaction. The number of myocardial segments demonstrating LGE was also quantitated, and the acquisition time of each PSIR sequence was performed.</p> <p>To our knowledge this is the first study that compares the 3 available PSIR LGE sequences with a specific attention to acquisition time (TA). Given our initial study resulted in the conclusion that the motion-corrected SSFP PSIR sequence was superior the the TurboFLASH Gradient Echo PSIR sequence in regards to evaluator grading and acquisition time efficiency.</p>
Sequences, taxonomic assignments, and R script from Comparison of Lava Cave Bacterial Mat Communities to Overlying Surface Soil Bacterial Communities from Lava Beds National Monument, USA
<p>This set of files contain the 16S rDNA, taxonomic assignments from the greengenes database, and the R script for processing the data. </p> <p><strong>Abstract</strong></p> <p>Lava caves around the world often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. We generated and analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soils overlying each cave. <em>Actinobacteria</em> dominated in all samples, with 39% (caves) and 21% (surface soils). <em>Proteobacteria</em> made up 30% of phyla from caves and 36% from surface soil with <em>Gamma</em>- 20% and <em>Alpha</em>- 10% in the caves and <em>Gamma</em>- 18% with <em>Alpha</em>-17% in soil. Other major phyla in caves were <em>Nitrospirae</em> (7%) followed by Minor Phyla (7%), compared to surface soils with <em>Bacteriodetes</em> (8%) and Minor phyla (8%). A very high proportion (53.33%) of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. The same phyla were represented in both soils and cave microbial mats, but the overlap was only 11.2% at the operational taxonomic unit (OTU). Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. In terms of species richness, diversity by mat color differed, but not significantly. Number of entrances per cave, distance from an entrance, cave length, and temperature also contributed to observed differences in diversity. With high levels of novel microbes, caves may represent excellent habitats for the isolation of new bioactive compounds. This study is the first comprehensive comparisons of bacterial communities in lava caves with the overlying soil community.</p>
Runway sequencing benchmarks for Manchester Airport
<p>Runway sequencing benchmarks for Manchester Airport for various traffic densities</p>
The Free-Breathing Motion-Corrected Phase Sensitive Inversion Recovery Sequence Provides Improved Myocardial Fibrosis Evaluation while Significantly Shortening Acquisition Time Compared to Conventional Gradient Echo Sequences.
<p>This article includes original research performed at a US Academic Center related to comparison of three separate Phase-Sensitive Inversion Recovery (PSIR) pulse sequences (Breath-hold Single-Shot SFFP, Breath-hold TurboFLASH, and Free-breathing Motion-Corrected SSFP) evaluating the ability of each PSIR sequence to demonstrate myocardial hyperenhancement. All three PSIR sequences were performed as a part of a cardiac MRI performed on a patient clinically referred for cardiac MRI with and without contrast. A total of 28 patients were examined with the three PSIR sequences. All three PSIR sequences were performed in the short axis 10 – 25 minutes after intravenous injection of a Gadolinium-based contrast agent. </p> <p>Evaluation of the PSIR sequences ability to detect myocardial late gadolinium enhancement (LGE) was performed by a retrospective review by two blinded, experienced cardiovascular imagers. The review was a qualitative inspection that included grading by a 5-point Likert scale for the sequence’s ability to resist motion artifact, image resolution, ability to visualize hyperenhancement, and overall satisfaction. The number of myocardial segments demonstrating LGE was also quantitated, and the acquisition time of each PSIR sequence was performed.</p> <p>To our knowledge this is the first study that compares the 3 available PSIR LGE sequences with a specific attention to acquisition time (TA). Given our initial study resulted in the conclusion that the motion-corrected SSFP PSIR sequence was superior the the TurboFLASH Gradient Echo PSIR sequence in regards to evaluator grading and acquisition time efficiency.</p>
Aligned and trimmed 16S and COI DNA sequences of Oceaniidae (Hydrozoa)
<p>Aligned and trimmed 16S and COI sequences of Oceaniidae (Hydrozoa) used for the study "The polyps of <em>Oceania armata</em> identified by DNA barcoding (Cnidaria, Hydrozoa)"</p> <p>Format is Fasta, files are text files</p>
Training material for RNA sequencing
<p><strong>RNA-seq</strong> (<strong>RNA sequencing</strong>) uses high-throughput (HTS) data to reveal the presence and quantity of RNA in a biological sample at a given moment in time.</p> <p>RNA-Seq is used to analyze the continually changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression.<sup>[4]</sup> In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling.</p>
Training material for RNA sequencing
<p><strong>RNA-seq</strong> (<strong>RNA sequencing</strong>) uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment in time.</p> <p>RNA-Seq is used to analyze the continually changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression.<sup>[4]</sup> In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling.</p>
Training material for exome sequencing
<p>Exome sequencing means that all protein-coding genes in a genome are sequenced.</p> <p>In Humans, there are ~180,000 exons that makes up 1% of the human genome which contain ~30 million base pairs. Mutations in the exome have usually a higher impact and more severe consequences, than in the remaining 99% of the genome.</p> <p>With exome sequencing, one can identify genetic variation that is responsible for both Mendelian and common diseases without the high costs associated with whole-genome sequencing. Indeed, exome sequencing is the most efficient way to identify the genetic variants in all of an individual's genes. Exome sequencing is cheaper also than whole-genome sequencing. </p> <p> </p> <p>For training on exome sequencing data analysis, the Galaxy community proposes two tutorials (https://github.com/bgruening/training-material/tree/master/Exome-Seq). Here, you can find the needed datasets for these tutorials.</p>
Sequence of snow maps produced from Sentinel-2 type of observations (SPOT-5 Take 5) over the Deux Alpes and Alpe d'Huez ski resorts
<p>This is a series of snow cover maps between April 11 and September 8, 2015 over a region that covers the Deux Alpes and Alpe d'Huez ski resorts in France. The snow maps were produced from a SPOT-5 Take 5 images using the "Let-it-snow" processor (v1.0, June 2016: http://tully.ups-tlse.fr/grizonnet/let-it-snow).</p> <p>The SEB folder contains 20 GeoTiff at 10 m résolution in Lambert-93 projection system coded as follows (cf. http://tully.ups-tlse.fr/grizonnet/let-it-snow#products-format):</p> <p> 0: No-snow<br> 100: Snow<br> 205: Cloud including cloud shadow<br> 254: No data</p> <p>The "anim_no05jul_opt" animated gif was produced from these data after performing a simple temporal interpolation given by the following rules:</p> <ul> <li>If a pixel masked by a cloud was marked as snow in the preceding image and in the following image, then it is reclassified as a snow pixel.</li> </ul> <ul> <li>If a pixel masked by a cloud was marked as no-snow in the preceding image and in the following image, then it is reclassified as a no-snow pixel.</li> </ul> <p>The July 05 image was removed from the animation due to a cloud/snow confusion. This type of error should be avoided with Sentinel-2 data thanks to an additional "high cloud" test (see http://tully.ups-tlse.fr/grizonnet/let-it-snow/blob/master/doc/tex/ATBD_CES-Neige.pdf).</p> <p>These data were featured in this blog post : Gascoin, S. "Monitoring the snow cover in ski resorts using Sentinel-2" (19-Sep-2016) http://www.cesbio.ups-tlse.fr/multitemp/?p=8676</p>
Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?
<p>The 8 benthic samples from Mainland France (stream Edian, stream Aire, lake Geneva), Sweden (stream Dåmman, Agricultural stream, lake Båtkåjaure) and Mayotte (stream Dapani, stream Majimbini) were collected by scraping material from the surface of stones, following the French standard (AFNOR 2007) used in routine biomonitoring programs.DNA was extracted from each sample (2 replicates) using five DNA extraction methods, followed by the amplification of a short rbcL DNA barcode (312bp) specific to diatoms. PCR products were then sequenced in one random direction using the Ion Torrent™ Personal Genome Machine® (PGM) System according to the manufacturer’s instructions. The data file contains one fastq file per library sequenced with the raw DNA reads, as provided by the sequencing platform (demultiplexing performed by the sequencing platform). An excel file is also provided to make the link between the fastq file number and the sample information (sample origin, DNA extraction method used, number of raw reads).</p>
Sequence data for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol" - single cells dataset
<p>Sequence data (Illumina MiSeq runs) for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol". dataset of 2300 single cells. File names indicate unique sequencing runs. In the manuscripts, the informations about cell lines are found in the Supplemental Table 1. </p>
Sequence data for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol" - Protocol optimization
<p>Sequence data (Illumina MiSeq runs) for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol". Optimization of the protocol. Files names indicate unique run identifiers. In the manuscript, the link between unique run identifiers, cells and purpose of the experiment is found in the Supplemental Table 1. </p>
ScienceDex guides
Understand access before you commit
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.