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54 results for “synthetic genomics”
Genome of the isolates: Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities
<p>The draft genome of the isolates in Mouse Intestinal Bacteria Collection (miBC)</p> <p> </p> <p>Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. Due to host-specific features of the gut microbiota, it is sound to establish collections of isolates from single host species. Hence, this project established a collection of bacterial strains isolated from the intestine of mice.</p> <p>The original version of the collection published in 2016 (Lagkouvardos, et. al. 2016.<em> Nat. Microbiol.</em>). was doubled by the addition of 112 strains, representing a total of 141 species across 6 phyla and 35 families for the entire collection. As we aimed to create a well-curated resource, all bacterial species within miBC have been taxonomically described and are publicly available.</p> <p> </p>
Shotgun metagenomic sequencing dataset of a synthetic mock community containing 20 genomes spiked-in at even and staggered concentrations.
<p>Shotgun metagenomics (SM) sequencing is a popular method used in microbial ecology to obtain insights on microbial community structure and function potential in a given biological system without the need to cultivate microorganisms. The dataset described in this article describes technical triplicates of shotgun metagenomic sequence libraries generated from two purified and titrated mixes of 20 distinct reference bacterial genomes for which key characteristics such as genome size, sequence and spiked-in concentrations are known. In one of the genomic DNA mix, each genome is spiked-in at similar concentrations (representing an even microbial community) and in the other, genomes are spiked-in at different concentrations with some genomes highly abundant and other in low quantity, mimicking an uneven microbial community DNA extract. In order to be interpretable, SM sequencing data needs to be properly analyzed by complex analytical bioinformatic pipelines. Environments investigated with this method can range from simple to very complex. Typically, microbial communities contain microbes that are ubiquitous and some others much rarer. Analysis of rare microbes in a complex microbial community are challenging to perform as their sequencing signals get submerged by the microbial genomes that are more abundant. In this context, it is critical to have access to sequencing data of simple mock communities of mixes of well characterized genomes in order to develop and validate bioinformatic methods that aim to accurately analyze microbial communities.</p>
Data from: Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria
PREMISE OF THE STUDY Divergence in functional traits and adaptive responses to environmental change underlies the ecological advantage of polyploid plants in the wild. While established polyploids may benefit from combined outcomes of genome doubling, hybridization and polyploidy-enabled adaptive evolution, it remains less clear whether genome doubling alone can drive ecological divergence or whether the outcome is genetically variable.METHODS Using synthetic, colchicine-induced, autotetraploid (4x) plants derived from self-pollinated diploid (2x) seeds, and their colchicine-treated but unconverted diploid (2x.nc) full sibs from two diploid wild strawberry taxa (Fragaria vesca ssp. vesca and F. vesca ssp. bracteata), we examined the effects of genome doubling on functional traits, heat stress tolerance and fitness components across taxa and maternal families (i.e. genetic families) within taxa.KEY RESULTS Comparisons between 2x and 2x.nc plants indicated a negligible effect of colchicine treatment on functional traits. Genome doubling increased stomatal length, and decreased stomatal density, specific leaf area and leaf vein density, recapitulating patterns observed in wild polyploid Fragaria. Trichome density, heat stress tolerance and relative growth rate were not significantly affected by genome doubling. Although a reduction in clonal reproduction was observed in response to genome doubling, this effect was strongly genetic family dependent.CONCLUSIONS The results suggest that genome doubling during incipient speciation alone can generate ecological divergence and variation among genetic lineages. This response potentially allows for rapid short-term evolutionary adaptation and fuels genomic diversity and independent origins of polyploidy.
Data from: Genome-wide CRISPR synthetic lethality screen identifies a role for the ADP-ribosyltransferase PARP14 in replication fork stability controlled by ATR
<p>The DNA damage response is essential to maintain genomic stability, suppress replication stress, and protect against carcinogenesis. The ATR-CHK1 pathway is an essential component of this response, which regulates cell cycle progression in the face of replication stress. PARP14 is an ADP-ribosyltransferase with multiple roles in transcription, signaling, and DNA repair. To understand the biological functions of PARP14, we catalogued the genetic components that impact cellular viability upon loss of PARP14 by performing an unbiased, comprehensive, genome-wide CRISPR knockout genetic screen in PARP14-deficient cells. We uncovered the ATR-CHK1 pathway as essential for viability of PARP14-deficient cells, and identified regulation of DNA replication dynamics as an important mechanistic contributor to the synthetic lethality observed. Our work shows that PARP14 is an important modulator of the response to ATR-CHK1 pathway inhibitors.</p>
TP53 synthetic genomics data for benchmarking variant callers
<p>This is a synthetic genomics dataset generated with <a href="https://github.com/ncsa/NEAT">NEAT </a> for the gene TP53 for the use case of benchmarking somatic variant callers. The reports for all bam files where created using <a href="https://github.com/genome/bam-readcount">bam-readcount</a>.</p> <p>To find out more about our pipeline please visit <a href="https://github.com/BiodataAnalysisGroup/synth4bench">the Biodata Analysis Group GitHub</a> and also our <a href="https://biodataanalysisgroup.github.io/">GitHub page</a> :)</p>
Designing a Synthetic Microbial Community through Genome Metabolic Modeling to enhance Plant-Microbe Interaction
<p>Supplementary data 1 - <strong>Reconstructed genome-scale metabolic networks from MAGs and Hosts</strong></p> <p>Supplementary data 2 - P<strong>lant growth-promoting traits among members of the minimal community</strong></p> <p> </p> <p>Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynCom, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and a careful selection of compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed an <em>in-silico</em> approach using genome metabolic modeling to design a synthetic microbial community aimed at improving the yield of important crop plants. We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, EPS production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our selection process for the SymCom, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. Our study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.</p>
Data from: Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria
Open the record for dataset details and reuse information.
Data from: Genome-wide CRISPR synthetic lethality screen identifies a role for the ADP-ribosyltransferase PARP14 in replication fork stability controlled by ATR
Open the record for dataset details and reuse information.
Synthetic Noisy Reads Generated from Human Genomes
<p>This repository contains datasets with size 200K, 400K and 1 Million noisy reads generated from 5000 transcripts of GTcenters.fasta file. The assigned task is to recover the ground-truth transcripts (GTcenters) based on the given noisy reads.</p>
Genome-wide synthetic lethal screen unveils novel CAIX – NFS1/xCT axis as a targetable vulnerability in hypoxic solid tumors.
GEO Series GSE167481. Homo sapiens. 8 samples. Type: Other.
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers [Drosophila genome-wide UMI-STARR-seq]
GEO Series GSE183936. Drosophila melanogaster; synthetic construct. 6 samples. Type: Other.
Genome-Wide CRISPR Screen Identifies Multiple Synthetic Lethal Targets That Enhance KRAS (G12C) Inhibitor Efficacy [CRISPR]
GEO Series GSE240110. Homo sapiens. 36 samples. Type: Other.
A genome-scale screen for synthetic drivers of T-cell proliferation
GEO Series GSE193736. Escherichia coli; Homo sapiens. 44 samples. Type: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide synthetic lethal CRISPR screen identifies FIS1 as a genetic interactor of ALS-linked C9ORF72
GEO Series GSE142504. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing; Other.
Analysis of the overlapping tri-nucleosome association with genomic and synthetic DNA
GEO Series GSE224789. synthetic construct; Homo sapiens. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Discovery of synthetic lethal and tumor suppressive paralog pairs in the human genome
GEO Series GSE178179. synthetic construct; Homo sapiens. 12 samples. Type: Other.
Genome-Wide CRISPR Screen Identifies Multiple Synthetic Lethal Targets That Enhance KRAS (G12C) Inhibitor Efficacy [RNA-seq-mm10]
GEO Series GSE240113. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
A barcoded genome-scale library of inducible alleles reveals principles of synthetic gene control
GEO Series GSE158319. Saccharomyces cerevisiae. 357 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing; Other.
Genome-wide CRISPR screen identifies cell cycle as a synthetic lethal pathway with SRSF2P95H mutation
GEO Series GSE165505. Mus musculus. 24 samples. Type: Other.
Cycling transcriptional networks reduce the synthetic cost of genomes
GEO Series GSE57683. Saccharomyces cerevisiae. 44 samples. Type: Expression profiling by high throughput sequencing.
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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.