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Dataset results
99 results for “bacterial genome”
Unlock the mystery of the hard-to-sequence phage genome: discovering a novel mechanism of bacterial immunity
GEO Series GSE50100. Pseudomonas phage PaP1. 1 samples. Type: Methylation profiling by high throughput sequencing.
REPARATION: Ribosome Profiling Assisted (Re-) Annotation of Bacterial genomes
GEO Series GSE91066. Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
Non-canonical base modifications of bacterial origin in a eukaryotic genome [MeDIP-seq]
GEO Series GSE140050. Adineta vaga. 4 samples. Type: Methylation profiling by high throughput sequencing.
Non-canonical base modifications of bacterial origin in a eukaryotic genome [ChIP-seq]
GEO Series GSE140049. Adineta vaga. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study
GEO Series GSE65088. Homo sapiens. 57 samples. Type: Expression profiling by array.
A dual-genome microarray for the pea aphid, and its obligate bacterial symbiont
GEO Series GSE3742. Buchnera aphidicola; Acyrthosiphon pisum. 1 samples. Type: Expression profiling by array.
Data from: Efficient inference of recombination hot regions in bacterial genomes
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of "hotspots" of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here we focus in particular on identifying "hot regions" of the genome where DNA is transferred frequently between isolates. We present a computationally efficient algorithm based on the recently developed "chromosome painting" algorithm, which characterizes patterns of haplotype sharing across a genome. We compare the average genome wide painting, which principally reflects clonal descent, with the painting for each site which additionally reflects the specific deviations at the site due to recombination. Using simulated data, we show that hot regions have consistently higher deviations from the genome wide average than normal regions. We applied our approach to previously analysed Escherichia coli genomes, and revealed that the new method is highly correlated with the number of recombination events affecting each site inferred by ClonalOrigin, a method that is only applicable to small numbers of genomes. Furthermore, we analysed recombination hot regions in Campylobacter jejuni by using 200 genomes. We identified three recombination hot regions which are enriched for genes related to membrane proteins. Our approach and its implementation, which is downloadable from https://github.com/bioprojects/orderedPainting, will help to develop a new phase of population genomic studies of recombination in prokaryotes.
Long read genome assembly of species from the synthetic HAMBI bacterial community
<p>We present complete genome sequences of 30 bacterial species that can be used to construct defined synthetic communities that stably form in the laboratory under controlled conditions.</p><p>This repository contains the final genome assemblies, logs, reports/summaries, scripts, and associated computational methods. All genomes were circularized (or in the case of <i>Agrobacterium tumefaciens</i> properly linearized) with the recovery of some small plasmids.</p><p>30 Species from the HAMBI community were sent for Oxford Nanopore or PacBio HiFi sequencing at <a href="https://www.seqcenter.com/">SeqCenter</a> early November 2022. I assembled multiple subsets of the read data for each genome and generated consensus assemblies using <a href="https://github.com/rrwick/Trycycler">Trycycler</a>.</p><p>All sequence data is available under BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1047486">PRJNA1047486</a></p><p>This is a mirror of the repository here: <a href="https://gitlab.utu.fi/slhogl/hambiLongRead">https://gitlab.utu.fi/slhogl/hambiLongRead</a></p>
Sepsis-dectection bacterial genomes dataset (TargetCall-D4)
<p>Detailed description:</p> <p>The fast5 files in this dataset is generated from ONT machine.</p> <p>This dataset includes the 15200 fast5 files sampled from paper: Performance of Neural Network Basecalling Tools for Oxford Nanopore Sequencing</p>
Viral-dectection bacterial genomes dataset (TargetCall-D3)
<p>Detailed description:</p> <p>The fast5 files in this dataset is generated from ONT machine.</p> <p>This dataset includes the 72567 fast5 files sampled from paper: Performance of Neural Network Basecalling Tools for Oxford Nanopore Sequencing</p>
Comparative genomics analysis of the aromatic and xenobiotic degradation capacities and heavy metal resistance in seven environmentally-derived bacterial isolates.
<p>Annotations and datasets generated from the comparative genomics analyses.</p>
Genome-wide screen of Mycobacterium tuberculosis-infected macrophages revealed GID/CTLH complex-mediated modulation of bacterial growth
GEO Series GSE267063. Mus musculus; Mycobacterium tuberculosis. 12 samples. Type: Expression profiling by high throughput sequencing.
Data from: Efficient inference of recombination hot regions in bacterial genomes
Open the record for dataset details and reuse information.
Genome-wide identification of Hfq-regulated small RNAs in the bacterial pathogen Erwinia amylovora
GEO Series GSE53763. Erwinia amylovora. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Characterization of Bacterial Transcriptional Regulatory Networks in Escherichia coli through Genome-Wide In Vitro Run-Off Transcription/RNA-seq (ROSE)
GEO Series GSE159312. Escherichia coli. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
A chromosomal loop anchor mediates bacterial genome organization
GEO Series GSE144475. Bacillus subtilis. 30 samples. Type: Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing.
Microarray analysis of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation: genomic DNA
GEO Series GSE17517. Archaea; Bacteria; Escherichia coli. 38 samples. Type: Other.
Genome-wide identification of bacterial membrane protein expression determinants
GEO Series GSE95857. Escherichia coli BW25113. 94 samples. Type: Other.
Characterization of the Bacterial Diversity of Drinking Water From 3 Parisian Treatment Plants Using Genomic Approaches
GEO Series GSE14318. Bacteria. 3 samples. Type: Other.
Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens
GEO Series GSE103117. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
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.