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660 results for “Genome assemblies”
A genomic regulatory element that directs assembly and function of immunespecific AP-1-IRF complexes
GEO Series GSE40483. Mus musculus. 15 samples. Type: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing.
Homology-guided Assembly of the Genomes of the Four Diverse Accessions Ler, C24, Bur-0 and Kro-0
GEO Series GSE24569. Arabidopsis thaliana. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa
GEO Series GSE132939. Populus trichocarpa. 85 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability [RNA-seq]
GEO Series GSE114946. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with contrasting susceptibilities to Ralstonia solanacearum
GEO Series GSE255584. Solanum nigrum. 1 samples. Type: Methylation profiling by high throughput sequencing; Other.
Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome.
GEO Series GSE127823. Steinernema carpocapsae. 33 samples. Type: Expression profiling by high throughput sequencing.
Alternate genome assemblies of Halicephalobus mephisto
<p>Alternate genome assemblies were generated using Illumina data from a published study (Weinstein et al, 2019) publicly available on Sequence Reads Archive (SRA) at accession PRJNA528747. Assemblies were generated with either Platanus or SoapDenovo2 using varying step-sizes (Platanus) or kmers (SoapDenovo2) and using either a 1kb or 200bp cutoff on scaffold lengths. These assemblies were then analyzed in a separate study (under review) to identify regional expansions or contractions associated with high levels of heterozygosity.</p> <p>Cited:</p> <p>Weinstein, D.J., Allen, S.E., Lau, M.C.Y. <em>et al.</em> The genome of a subterrestrial nematode reveals adaptations to heat. <em>Nat Commun</em> <strong>10, </strong>5268 (2019). https://doi.org/10.1038/s41467-019-13245-8</p>
Genome assembly of Malassezia pachydermatis isolated from a canine otitis clinical sample
<p>We report the raw signal data output obtained from a <em>Malassezia pachydermatis</em> isolate of a canine clinical sample (otitis). Multiple barcoded samples run was performed with the MinION device, Oxford Nanopore Technologies, and the barcode02 was assigned to this sample. The raw signal data, fast5 files (showed in the Fats5.zip directory), were basecalled and demultiplexed in order to achieve the fastq file format which includes only the sequences targeted with barcode02 (M13_UAB2019.fastq).</p>
Chromosome-level genome assembly of Chinese mitten crab (Eriocheir japonica sinensis)
<p>The Chinese mitten crab (<i>Eriocheir japonica sinensis</i>) is one of the most popular breeding species of crab in China due to its high economic and nutritional value. However, earlier published genome assemblies of <i>E. j. sinensis</i> have been highly fragmented due to limited sequencing and assembly techniques.<b> </b>In this study, we performed high-coverage sequencing of the Chinese mitten crab using advanced high-through chromosome conformation capture (Hi-C) technology and anchored these Hi-C data to previously published contig-level genome assembly for chromosome construction. Thus, we successfully assembled the first chromosome-level reference genome of <i>E. j. sinensis</i>, which contained 72 chromosomes with a N50 length of 17.61 Mb. Evaluation results demonstrated a high degree of genomic connectivity and accuracy. Acquisition of the chromosome-level genome of <i>E. j. sinensis </i>not only provides a basis for the study of adaptive evolution in crabs by comparative genomics, but should also help in studies on the growth, development, and reproduction of the Chinese mitten crab.</p>
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>
Genome assembly and annotations of Yoshiicerus persimilis
<p>Gene duplication is an important mechanism for organism evolution and adaptation. Whole-genome duplication (WGD) is considered as a major driver of species diversification. It has been reported that ancient WGD events occurred during the evolution of basal hexapod; the inferred pattern based on gene-tree and molecular-clock analyses remains challenging. Therefore, the lack of chromosome-scale genome has limited the characterization of WGD directly upon the synteny evidence. In order to get direct evidence from intra-chromosome synteny, we constructed the first chromosome-level genome of basal hexapod (<i>Yoshiicerus persimilis</i>, Collembola). We observed only large-scale gene duplications in chromosome 1, but not within/among other five chromosomes. These duplications were involved in proliferation and growth.</p>
Hybrid genome assemblies for 49 natural isolates of E.coli.
<p>Hybrid genome assemblies for 49 natural isolates of <em>E.coli. </em></p> <p>Assemblies were generated using Illumina and Oxford Nanopore long read data and each of the five assemblers, Canu, Flye, Raven, Redbean and Unicycler. </p>
Metagenome-assembled genomes from two genera of pitcher plants and three freshwater lakes
<p>Illumina shotgun metagenome sequences from <em>Sarracenia </em>and <em>Nepenthes </em>pitcher plants (originally published in Bittleston et al. 2018, MG-RAST RRID: SCR_004814; mgp15454) and three freshwater lakes (Consensus Lake, New York, USA (SRR15064816), Lake Mendota, Wisconsin, USA (SRR11647637), and Lake Samiti, Sikkim, India (SRR10757258)) were binned using CONCOCT v1.1.0 (Alneberg et al. 2014). Bins were further refined using anvi’o’s interactive interface v7.1 (Eren et al. 2015).</p>
De novo assembly of the polyhydroxybutyrate (PHB) producer Azohydromonas lata strain H1 (Pelleroni and Pelleroni, 1978) genome and genomic analysis of PHB production machinery
Open the record for dataset details and reuse information.
Four genome assemblies of legacy Xanthomonas oryzae pv. oryzae isolated from Indian rice fields
<p>This dataset contains sequencing data for <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> strain M24, including Illumina reads (SRR30576374) and PacBio HiFi reads (SRR30576370) from a genome announcement titled, "Four genome assemblies of legacy <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> isolated from Indian rice fields."</p>
Genome and transcriptome assemblies of TIL11
<p>Here, we employed single-molecule long-read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 non-redundant transcript isoforms. 23,527 predicted genes were identified using our state-of-the-art, machine learning-based bioinformatics pipeline DenovoAS_Finder without a complete reference genome. Additionally, we constructed a draft TIL11 genome based on a Nanopore sequencing dataset with 16,633 high-quality contigs and a N50 of 112 kb.</p>
Dataset for chromosome-level genome assembly of Scapharca kagoshimensis
<p>Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of <i><span>Scapharca kagoshimensis</span></i>, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells.</p>
Aspergillus flavus draft genome assemblies
<p>225 genome assemblies of <em>Aspergillus flavus</em> isolates.</p>
Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity - ASSEMBLIES [INTERNATIONAL] - Data S1
<p>Macroalgae are a polyphyletic group of multicellular aquatic organisms vital to global climate maintenance and have a wide variety of commercial applications. The lack of genomic datasets and poor physiological records preclude understanding their ecological roles and industrial potential. We <em>de novo</em> sequenced 121 macroalgal genomes from various climates spanning five major latitude parallels. The resultant genomic datasets reveal genetic bases for niche habitation facilitated by morphological complexity in diverse and extreme regions and illuminate the evolutionary mechanisms behind macroalgal diversification and specialization. Adhesome genes (e.g., cadherins, integrins, and lectins), extracellular matrix enzymes, and cytoskeletal organization regulating genes (e.g., spondins, Rho-type GTPases) predominantly distinguished macroalgal genomes from their microalgae correlates. Deep neural networks could accurately classify an alga as micro- or macro- from set of significance-ranked genomic features (n = 251, entropy R<sup>2</sup> > 0.99, RASE = 0.001) as well as adhesome gene sets (n = 110, entropy R<sup>2</sup> > 0.86). By deciphering the macroalgal adhesome, a clear picture of the genetic basis for the development and maintenance of complex algal tissues could be resolved. Sequences from giant viruses were rampant in the macroalgal genomes and coded for zinc-finger transcription factors, ankyrins, Rieske proteins, and other exotic codomains. Lineage-specific retentions of transcription factors, cadherins, integrins, polysaccharide-acting enzymes, and receptor kinases, many with predicted viral origins, outline the divergent mechanisms facilitating multicellularity in these three macroalgal lineages. This work sheds new light on the evolution of multicellularity in three phyla (Rhodophyceae, Chlorophyceae, and Ochrophyceae v. Phaeophyceae) through the lens of large-scale genomics and paves the way for the genomic exploration of macroalgal biology.</p>
Chromosome-Level Genome Assembly of the 'Gannanzao' Navel Orange (Citrus sinensis L. Osbeck Gannanzao)
<p>Gannanzao navel orange (<em>Citrus sinensis</em> Osbeck cv. Gannanzao) is a variant of the Newhall navel orange (<em>C. sinensis</em> Osbeck cv. Newhall) that exhibits an earlier maturation, making it commercially valuable. However, the underlying mechanism underneath its early maturation remains unknown. To address this question, we conducted genome sequencing and de novo assembly of navel orange cv. Gannanzao. The assembled genome sequence is 334.57 Mb in length with a GC content of 31.48%. It comprises 318 contigs (N50 = 3.23 Mb) and 187 scaffolds (N50 = 31.86 Mb). The BUSCO test demonstrates 94.6% completeness. The annotation revealed 23,037 gene models, 164.95 Mb of repetitive sequences, and 2,554 ncRNA.</p>
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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.