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63 results for “ncbi”
Metrics: NCBI data coverage
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Metagenomic and metatranscriptomics data for Bathymodiolus mussel and deep-sea sponge associated symbionts deposited in NCBI, IMG and other databases
<p>Metagenomic data for the sulfur- and methane-oxidizing symbionts of <em>Bathymodiolus</em> mussels and different sponge species deposited in the Integrated Microbial Genomes (IMG) database of the DOE Joint Genome Institute (http://img.jgi.doe.gov/) and NCBI until October 2018</p>
NCBI Virus BLAST Database
<p>Curated database of NCBI virus genomes, formatted for BLASTn</p>
Data for NCBI BioProject PRJNA966929
<p>Data for NCBI BioProject PRJNA966929: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA966929">Total Shark microbiome 16S</a></p> <p>We here analyzed bacterial communities associated with different microenvironments associated with wild-caught black-tip reef sharks (<em>Carcharhinus melanopterus</em>), specifically the body surface, oral/buccal cavity, and the cloaca in comparison to the water column from the Amirante Islands, Seychelles, using 16S rRNA gene amplicon sequencing and inferred their putative functions.</p> <p><em>Description:</em></p> <p><strong>Supplementary Table S2. </strong>16S rRNA gene sequence counts distributed over amplicon sequence variants (ASVs) and samples (shark and seawater samples), including taxonomic annotation and representative sequences; low abundant sequences (< 10 sequences in total across all samples) and contaminants were removed.</p> <p><strong>Supplementary Table S3.</strong> Results of multi- and univariate test statistics of bacterial community composition and diversity indices associated with seawater and microenvironments associated with blacktip reef sharks (<em>Carcharhinus melanopterus</em>) from the Amirante Islands, Seychelles. <strong>A.</strong> Results of Permutational Analysis of Variances (PERMANOVA) with seawater samples included. <strong>B.</strong> Results of Permutational Analysis of Variances (PERMANOVA) following the exclusion of seawater samples due to significant multivariate dispersion, and subsequent adonis PERMANOVA on bacterial communities of shark-associated microenvironments. <strong>C.</strong> Results of Similarity Percentages Breakdown (SIMPER) analysis to identify ASVs significantly contributing to dissimilarity in bacterial communities associated with different microenvironments. headers: sd = standard deviation; ratio = average to sd ratio; ava,b = average abundances per groups compared; cumsum = ordered cumulative contribution. <strong>D.</strong> Linear regression and pairwise test results of differences in alpha diversity indices associated with bacterial communities in seawater and the four different shark-associated microenvironments. <strong>E.</strong> Calculated Alpha diversity indices associated of bacterial communities in seawater and four different microenvironments on and in the body of blacktip reef sharks (<em>Carcharhinus melanopterus</em>) from the Amirante Islands, Seychelles. </p> <p><strong>Supplementary Table S4.</strong> Results of indicator taxa analysis to assess ASVs significantly associated with individual microenvironments or combinations of bacterial microenvironments on black-tip reef sharks (<em>Carcharhinus melanopterus</em>) in the Amirante Islands, Seychelles.</p> <p><strong>Supplementary Table S5.</strong> Linear Discriminant Analysis Effect Sizes (LEfSe) to identify bacterial ASVs present at increased occurrences in seawater and in different microbial microenvironments associated with black-tip reef sharks (<em>Carcharhinus melanopterus</em>) from the Amirante Islands, Seychelles.</p> <p><strong>Supplementary Table S6</strong>. Output of PICRUSt2 analysis of bacterial community data (16S rRNA gene sequences) distributed across individual samples, specifically seawater and associated with black-tip reef sharks (<em>Carcharhinus melanopterus</em>) from the Amirante Islands, Seychelles. <strong>A</strong>. Predicted metabolic functions. Discriminant traits were determined using linear discriminant analysis (LDA) effect size method with a cut-off > 2.0 for each MetaCyc pathway. <strong>B</strong>. Overview of weighted Nearest Sequenced Taxon Index (NSTI) scores of bacterial ASVs.</p> <p><strong>Supplementary Table S7.</strong> Linear Discriminant Analysis Effect Sizes (LEfSe) of predicted metabolic (MetaCyc) pathways inferred from bacterial community data associated with seawater and different microbial microenvironments associated with black-tip reef sharks (<em>Carcharhinus melanopterus</em>) from the Amirante Islands, Seychelles.</p>
Centrifuge Index for NCBI RefSeq Viruses 2020-01-30
<p>Centrifuge index for NCBI RefSeq Viruses downloaded 2020-01-30</p>
NCBI GenBank bacterial sequence assemblies 1/4
<p>Bacterial genomes and scaffolds downloaded from the NCBI GenBank assembly database (part 1/4).</p>
NCBI GenBank bacterial sequence assemblies 2/4
<p>Bacterial genomes and scaffolds downloaded from the NCBI GenBank assembly database (part 2/4).</p>
NCBI RefSeq Escherichia coli sequence assemblies
<p>18 GB Escherichia coli sequences downloaded from the NCBI assembly database.</p>
NCBI GenBank bacterial sequence assemblies 4/4
<p>Bacterial genomes and scaffolds downloaded from the NCBI GenBank assembly database (part 4/4).</p>
NCBI GenBank bacterial sequence assemblies 3/4
<p>Bacterial genomes and scaffolds downloaded from the NCBI GenBank assembly database (part 3/4).</p>
Genome sequencing and assembly of Phytophthora oleae, isolate VK10A, NCBI sequences annotation.
<p>Annotation of the first draft of genome assembly of Phytophthora oleae, isolate code: VK10A.</p> <p>This isolate has been found in rot of mature olive drupes (Olea europaea var. sylvestris), from a tree located in Sicily: Complesso Speleologico Villasmundo S. Alfio Nature Reserve (NR) (Melilli, Siracusa, Italy); DATUM WGS 84, 37°13'17.2"N 15°06'22.3"E.</p> <p>Supplementary materials related to the manuscript: </p> <p><strong>Genome sequencing and assembly of <em>Phytophthora oleae</em>, isolate VK10A, causative agent of rot of olive drupes.</strong></p> <p><span>The Whole Genome Shotgun (WGS) of <em>P. oleae</em> genome assembly project has been deposited at DDBJ/ENA/GenBank under the accession JBIMZQ000000000 (assembly DJ1425, https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_046127205.1/).</span></p> <p> </p>
Kleb. p. NCBI top 20 seq
<p>This is a set of test data used for the Africa CDC Pathogen genomics klebsiella workshop</p>
Classification of the UBCF_13 COG based on COG database in NCBI
<p><b>Background:</b> The <i>Serratia plymuthica</i> UBCF_13 is a phylloplane associated plant bacterium showing antifungal activity. Whole genome sequence provides information to get more insight about evolutionary study, unique traits in the genome and possibility to explore potential of this microorganism for future study. Here, we report the genome sequence of <i>S. plymuthica </i>UBCF_13 and the comparison with other seventeen strain.</p> <p><b>Methods:</b> Continuous short reads were attained from Illumina sequencing runs and reads of 150 bp were merged into a single dataset. A pan-genome based method was used to identify the core-genome of <i>S. plymuthica </i>species and the unique gene in UBCF-13.</p> <p><b>Results:</b> Assembled Illumina reads of <i>S. plymuthica </i>strain UBCF_13 genome was produced a 5.46 Mb circular genome sequence. 3315 genes were found to belong to the core-genome sheared by the 18 strains evaluated. The UBCF_13 genome harbors 488 unique genes, where 300 of which only can be found in this strain. The raw and assembled data is available via NCBI Short Read Archive (accession Number: SRR15012717) and genome database (accession number: CP068771).</p>
Classification of the UBCF_13 COG based on COG database in NCBI
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Indexed hg38 human genome from NCBI
<p>Raw data obtained from https://www.ncbi.nlm.nih.gov/assembly/88331</p> <p>Processed using</p> <p>- bwa mem for indexing</p>
Effectiveness of Nurse-Conducted Brief Intervention (NCBI) Supplemented With Mobile for Preventing Alcohol Use Disorders
ClinicalTrials.gov study NCT06652802. IPD Sharing: YES. Countries: 0. Publications: 0.
NCBI GEO Submission of human whole blood transcriptomes in response to a high-fat meal
GEO Series GSE127530. Homo sapiens. 45 samples. Type: Expression profiling by high throughput sequencing.
Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy [placenta-ncbi-placenta-villi_multiomic]
GEO Series GSE247036. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy [placenta-ncbi-cell-line_ChIPseq_cuttag]
GEO Series GSE247035. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy [placenta-ncbi-cell-line_scRNA-seq_snRNA-seq]
GEO Series GSE247037. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
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.