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77 results for “Sequencing Results”
DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region
<p>This dataset has been prepared as part of the Interreg Alpine Space project Eco-AlpsWater (ASP569) - <em>Innovative Ecological Assessment and Water Management Strategy for the Protection of Ecosystem Services in Alpine Lakes and Rivers</em>, <a href="https://www.alpine-space.eu/projects/eco-alpswater/en/home">https://www.alpine-space.eu/projects/eco-alpswater/en/home</a></p> <p>Individual archives include 16S rRNA (cyanobacteria) and 18S rRNA (microalgae) FASTA sequences and associated blastn results obtained from the high throughput sequencing of plankton and biofilm bulk/eDNA samples collected in 2019 in 37 lakes and 22 rivers across the Alpine region. These are supporting files for the paper by Salmaso et al., 2022. DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region. Science of the Total Environment, in press.</p>
THOR RNA-sequencing results
<p>Summarized results of RNA-sequencing performed within THOR (targeting smooth muscle cells in atherosclerosis). THOR is a collaborative project of Aarhus University and Novo Nordisk A/S as a part of the Open Discovery Innovation Network (ODIN) initiative.</p> <p>See detailed data description in the file "DESCRIPTION.md".</p>
Dataset of backprojection and MT inversion results for 2023 Türkiye earthquake sequence
<p>This dataset contains the results of the back-projection analysis of the two Mw 7.7 and 7.6 earthquakes on February 6, 2023 in south-eastern Türkiye and the centroid moment tensor inversion results for one foreshock and 221 aftershocks. All methods and results are described in detail in the publication: Petersen et al., (2023): The 2023 SE Türkiye seismic sequence: Rupture of a complex fault network. The Seismic Record, 3 (2): 134-143. <a href="https://doi.org/10.1785/0320230008">https://doi.org/10.1785/0320230008</a></p>
Course 27255 - Subsampled Sequencing Results
<p>This dataset contains a subset of the raw fastq data of the microbial isolates collected during the course <strong>27255 - Advanced Experimental Prokaryotic Molecular Biology and Ecology (Spring 2022) </strong>at DTU.</p>
Course 27255 - Sequencing Results
<p>This dataset contains the raw fastq data of the microbial isolates collected during the course <strong>27255 - Advanced Experimental Prokaryotic Molecular Biology and Ecology (Spring 2022) </strong>at DTU.</p>
Mitochondrial DNA sequencing results control and MELAS fibroblasts. Povea-Cabello, S. et al 2022.
<p>Mitochondrial DNA sequencing results from control and MELAS patients-derived dermal fibroblasts. Povea-Cabello, S. et al 2022. </p>
Structural modelling results to accompany the paper "Uncommon mutational profiles of metastatic colorectal cancer detected during routine genotyping using next generation sequencing: an update"
<p>This repository contains the results of modelling missense mutants in KRAS, NRAS and BRAF observed in our study in the corresponding protein structures. Modelling was performed using FoldX.</p>
Sequencing results of the 21 resequenced herbarium tomato specimens
<p>Sequencing results of the 21 herbarium tomato specimens resequenced on an Illumina NovaSeq 600 platform.</p>
Accurate annotation of protein coding sequences with IDTAXA - classification results
<p>Raw classification results generated by IDTAXA, BLAST, and HMMER on a training set scraped from KEGG of > 1.5M sequences. HMMER and BLAST results are also converted into IDTAXA like objects for ease of comparison.</p>
Results from the revision of MultiSuSiE improves multi-ancestry fine-mapping in All of Us whole-genome sequencing data
<p>afr47041.zip, lat36378.zip, and eur115620.zip contain All of Us Summary Statistics used in the revised version of "MultiSuSiE improves multi-ancestry fine-mapping in All of Us whole-genome sequencing data". Summary statistics for three cohorts are included: Afr47k, Lat36k, and Eur116k. These cohorts have not been downsampled to have equal levels of missingness.</p> <p>pips.tsv contains fine-mapped variants with PIP > 0.01 via MultiSuSiE from the revised version of "MultiSuSiE improves multi-ancestry fine-mapping in All of Us whole-genome sequencing data". Subcohorts with the _unmatched suffix have not been downsampled to have equal levels of phenotyped missingness across ancestries. </p> <p>MultiSuSiE-main.zip contains the MultiSuSiE software packages (corresponds to the Github repo on 10/16/2025).</p> <p>Please cite:</p> <p>Rossen, Jordan, et al. "MultiSuSiE improves multi-ancestry fine-mapping in All of Us whole-genome sequencing data." <em>medRxiv</em> (2024): 2024-05.</p> <p> </p>
ASMC: sequence and result files
<p>This repository contains the data specified in the application note entitled "ASMC: investigating the amino acid diversity of enzyme active sites". It includes:</p> <p>1. *.fa.gz - The starting sequence sets in FASTA format.</p> <p>2. *_removed_sequences.txt.gz - The list of sequences discarded due to important gaps.</p> <p>3. *_groups_X_min_Y.tsv.gz - The ASMC results in TSV format. The columns must be read as follows: "Protein ID | Active Site sequences | ASMC group". The letters X and Y correspond to the DBSCAN parameters defined with the 'auto' option (eps and min_samples, respectively).</p>
Datasets of mineral composition and geochronological result of Barrovian metamorphic sequence rocks in the Ailao Shan massif
<p>This file includes the supporting information of the manuscript titled“Thermal and physical properties of Barrovian metamorphic sequence rocks in the Ailao Shan-Red River shear zone, and implications for crustal channel flow”</p>
TESTAR sequence results
<p>TESTAR test results datasets extracted with TESTAR tool using CODEO desktop application as System Under Test (SUT). These datasets have been generated to be used as an example to be automatically generated and introduced locally in DECODER PKM, from H2020 DECODER Project.</p> <p>TESTAR tool is an open source tool (www.testar.org) for automated testing through graphical user interface (GUI) currently being developed by the Universitat Politecnica de Valencia and the Open University of the Netherlands.</p> <p>CODEO (https://www.sysgo.com/codeo) is an Eclipse-based IDE that facilitates embedded applications development, by providing all the components software engineers need. The architecture configurations can be esaily done through the CODEO graphical tools.</p> <p>PKM is the Persistent Knowledge Monitor developed as main infrastructure from H2020 DECODER Project (www.decoder-project.eu) under grant agreement number 824231.</p> <p>As TESTAR explores automatically the SUT, it will use the Document Object Model (DOM) information extracted from MyThaiStar SUT, to generate and save a TESTAR State Model in the OrientDB graph database. This model contains information about the Widgets, States and Actions, that were found in the SUT.</p> <p>- ArtefactTestResults_codeo_74_2021-12-14_13h38m39s.zip: For DECODER project purposes, TESTAR test results knowledge has been summarized and referenced in an artifact JSON file to adapt to PKM input requirements.</p> <p>- CODEO_TestResults.zip: All the information obtained through the DOM is used graphically and semantically to create screenshots, logs and html reports that indicate how TESTAR has navigated in the exploration and indicates if any error has been detected. </p>
Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights
<p>Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. We evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the fecal microbiome of a model population of feral horses (Sable Island, Canada). Since 2007, this unmanaged population has been the subject of an individual-based, long-term ecological study. Using deep shotgun metagenomic sequencing, we determined the sequencing depth required to accurately characterize the horse microbiome. In comparing conventional versus high-throughput shotgun metagenomic library preparation techniques, we validate the use of more cost-effective lab methods. Finally, we characterize similarities between 16S amplicon and shallow shotgun characterization of the microbiome and demonstrate that the latter recapitulates biological patterns first described in a published amplicon dataset. Unlike amplicon data, we further demonstrate how shallow shotgun metagenomic data provide useful insights about microbiome functional potential which support previously hypothesized diet effects in this study system.</p>
FLAIR2 results from LRGASP R2C2 sequencing of Human WTC11 and Mouse ES cell lines
<p>FLAIR2 results from Oxford Nanopore sequencing of R2C2 libraries generated from Human WTC11 and Mouse ES cell lines from the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) (Pardo-Palacios et al. Nature Methods 2024). FLAIR2 high-confidence isoforms are provided for WTC11 and ES cells. For Mouse ES cells, sequence variants were identified with Longshot and incorporated into transcript isoforms using FLAIR2. These data are associated with the FLAIR2 publication (Tang et al. 2024)</p>
Analysis results for association study of long-term kidney transplant rejection using whole-exome sequencing
<p>Association study results for long-term kidney transplant rejection. Single-variant association results are provided as Plink output files. Meta-analysis results are provided as METAL output files. FDR results are sorted lists of the top association result from random sample label permutations and are included with the plink and meta-analysis results. SKAT and GSEA results are provided for gene and pathway level analyses, respectively.</p>
Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing.
<p>Data from study, protocol published at 10.5281/zenodo.5081880</p> <p><strong>Extended Data Table 1: TAC results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing. </strong>(BAL: bronchoalveolar lavage.) *Not included in validation numbers as duplicate at sub-species or genus level detection, **MecA was not included in validation numbers. TAC hits which did not pass the internal quality control standards required for reporting are indicated by (not reported). Samples which did not undergo sequencing indicated by <em>ND</em>. (✓) indicates low confidence hits from sequencing.</p>
Chamaeleo africanus DNA sequencing purity results and statistics
<p>Conservation of wildlife often depends on high quality molecular data to establish reliable species identification. Traditional approaches in extracting material (DNA) for phylogenetic studies on chameleons have relied on removed, euthanized or preserved/museum specimens, while field sampling usually takes the form of tail clippings from living individuals and their subsequent release. In this article, we propose an alternative to these approaches for field sampling, towards isolation of nuclear and mitochondrial DNA with oral (buccal) swabs, a methodology already been demonstrated as effective in other taxa. Options of sampling, storage, transport, extraction of DNA are presented and the quality and quantity of extracted material (using venipuncture as a positive control) was demonstrated as sufficient for downstream applications, including sequencing thereby presenting a practical field alternative. The advantages and limitations of this minimally invasive and non-destructive method applied to <em>Chamaeleo africanus</em> are further discussed.</p>
MIR142 Sanger sequencing results in MPNs
<p>To extend and complement knowledge about the occurrence and/or frequency of <em>MIR142</em> mutations in hematologic cancers, we sequenced <em>MIR142</em> in large panels of MPNs [including polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF), and chronic myeloid leukemia (CML)], blood disorders for which such mutations have never been tested, and in AML and CLL, for which the mutations have been reported. The dataset gathers Sanger sequencing results of the <em>MIR142</em> locus.</p>
Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights
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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
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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.