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199
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Dataset results
199 results for “Genome references”
Microarray-based comparative genomic profiling of reference strains of Actinobacillus pleuropneumoniae
GEO Series GSE11921. Actinobacillus pleuropneumoniae serovar 5b str. L20; Actinobacillus pleuropneumoniae. 33 samples. Type: Genome variation profiling by array.
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes
GEO Series GSE198197. Isoetes sinensis. 6 samples. Type: Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
GEO Series GSE30814. Arabidopsis thaliana. 48 samples. Type: Expression profiling by high throughput sequencing.
Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]
GEO Series GSE209815. Mus musculus. 5 samples. Type: Genome variation profiling by high throughput sequencing.
Human SUP-B15 cells: CNV compared to reference genome.
GEO Series GSE239416. Homo sapiens. 1 samples. Type: Genome variation profiling by array; Genome variation profiling by SNP array.
Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry
<p>(P0652) Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry</p> <p>Genotyping-by-sequencing (GBS) approaches have enabled routine high-density genome-wide DNA variant discovery in numerous agriculturally important species. Applications of GBS in octoploid (2n = 8x = 56) strawberry (Fragaria × ananassa) have been hindered by the absence of a reference genome for physically mapping DNA sequences; for discovering variants with sub-genome resolution, or effectively distinguishing homologous from homeologous variation. High-quality reference genome assemblies have recently emerged, supplying the foundation for this study, which focused on demonstrating the utility of GBS for calling sub-genome specific DNA variants in octoploid strawberry. To reduce genomic DNA complexity, double-digest protocols were tested on diverse accessions with two restriction enzyme combinations (PstI-MseI and HindIII-MseI). GBS libraries were sequenced on an Illumina HiSeq 4000 using a 150 bp paired-end protocol. For the purpose of this study, we describe the deployment of a flexible bioinformatic pipeline for GBS-facilitated variant discovery in octoploid strawberry. The percentage of uniquely mapped reads ranged from 51.41% for PstI-MseI to 55.56% for HindIII- MseI resulting in 1,591,764 and 2,362,556 unique locations, respectively. The number of discovered variants was 2.5-fold greater for HindIII-MseI (491,811) than PstI-MseI (199,486). The GBS protocols uncovered a dense genome-wide landscape of DNA variants for high- precision genetic mapping, identification of DNA variants associated with agriculturally important phenotypes, genomic-enabled breeding, and other applications in octoploid strawberry.</p> <p>Poster: PDF of poster and abstract for PAG 2018 (P0652)</p> <p>Figures: PNGs of figures on the poster</p> <p>Scrips: Txt files of SLURM scripts used to generate the follow .vcf files.</p> <p>- 8x_GBS_0_index: Uses BWA to index the reference genome (Edger et al 2019) for later use.</p> <p>- 8x_GBS_1_Demultiplex: Used Sabre to demultiplex fastq.gz files. Demultiplex_key_PE links individuals to their unique barcode.</p> <p>- 8x_GBS_2_Main: adapter removal, sequence alignment, and individual variant calling as a SLURM array. results in a .gvcf file for individuals.</p> <p>- 8x_GBS_3_Variant: population-level variant calling to a final .vcf file</p> <p>VCF: Two VCF files from the two enzyme experiments. H = HindIII-MseI; P = PstI-MseI</p>
Resources for gasAcu1-4, a new stickleback reference genome
<p><em>gasAcu1-4</em> is a new version of the stickleback reference genome. It only minorly differs from the 2017 Hi-C guided assembly by Peichel, Sullivan, Liachko, and White (https://doi.org/10.1093/jhered/esx058) to improve the subtelomeric <em>Pitx1</em> locus and the mitochondrial genome. We here present basic resources for utilizing this version of the reference genome: the fasta sequence of the assembly and liftOver chains for converting coordinates between this reference version and the original (Broad S1) <em>gasAcu1 </em>assembly (https://www.nature.com/articles/nature10944).</p> <p>This assembly can be visualized and other data downloaded via the Table Browser of the UCSC Genome Browser by copying the following track hub URL into the "My Hubs" tab at https://genome.ucsc.edu/cgi-bin/hgHubConnect: https://sbwdev.stanford.edu/kingsleyAssemblyHub/hub.txt.</p>
Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence/absence variations (PAVs). In this study, we present the draft de novo genome assembly of PHJ89, an Oh43-type inbred line. Using three separate reference genome assemblies (B73, PH207, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profile and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assembly. GWAS was conducted in the 942 inbred panel using both the SNP and expression data values to map sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, GWAS results for SCMV resistance using expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when using the B73 reference that contains the gene, but not when using the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated using three different reference genomes.
"A Privacy-protecting Environment for Child Transplants Health Related and Genomic Data Integration in the European Reference Network"
ClinicalTrials.gov study NCT07194057. IPD Sharing: NO. Countries: 3. Publications: 0.
Data from: Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
Open the record for dataset details and reuse information.
Resources for gasAcu1-4, a new stickleback reference genome
Open the record for dataset details and reuse information.
Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel
Open the record for dataset details and reuse information.
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes
GEO Series GSE198194. Isoetes sinensis. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes
GEO Series GSE198196. Isoetes sinensis. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Anaerobic growth in M9 + glucose + fumarate,genomic DNA reference
GEO Series GSE4374. Escherichia coli. 6 samples. Type: Expression profiling by array.
Anaerobic growth in M9 + glucose, genomic DNA reference
GEO Series GSE4373. Escherichia coli. 6 samples. Type: Expression profiling by array.
Comparative genomic profiling of reference strains and selected Canadian field isolates of A. pleuropneumoniae
GEO Series GSE14639. Actinobacillus pleuropneumoniae; Actinobacillus pleuropneumoniae serovar 5b str. L20. 74 samples. Type: Genome variation profiling by array.
ChIP-Seq with reference exogenous genome (ChIP-Rx) of wild-type MYC and mutant MYC in U2OS-MYC-KO cells
GEO Series GSE252696. Homo sapiens. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Stationary phase in LB, genomic DNA reference
GEO Series GSE4380. Escherichia coli. 6 samples. Type: Expression profiling by array.
Genome-wide array comparative genomic hybridization (aCGH) profiling of copy number variations (CNVs) in various dog breeds in comparison to a reference sample
GEO Series GSE40210. Canis lupus; Canis lupus familiaris. 53 samples. Type: Genome variation profiling by genome tiling array.
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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.