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720 results for “Identification data”
Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing
GEO Series GSE39025. Rhodopseudomonas palustris CGA009. 3 samples. Type: Expression profiling by high throughput sequencing.
Identification of putative biomarkers for Infantile Hemangiomas and Propanolol treatment via data integration
GEO Series GSE127487. Homo sapiens. 28 samples. Type: Expression profiling by array.
Identification of transcription factor binding sites from ChIP-seq data at high-resolution
GEO Series GSE40664. Drosophila melanogaster. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: Methyl-seq data for the identification of hap-ASM
GEO Series GSE79148. Homo sapiens. 13 samples. Type: Methylation profiling by high throughput sequencing.
An effective approach for identification of in vivo protein–DNA binding sites from paired-end ChIP-Seq data
GEO Series GSE16940. Arabidopsis thaliana. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Identification of RCC subtype-specific microRNAs – meta-analysis of high-throughput RCC tumor microRNA expression data [miRNA-Seq]
GEO Series GSE151423. Homo sapiens. 32 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Integrative analysis of transcriptomic data for the identification of biomarkers associated with T-cell activation in preterm birth
GEO Series GSE148402. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data
GEO Series GSE33383. Homo sapiens. 131 samples. Type: Expression profiling by array; Genome variation profiling by SNP array.
Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions using RNA-Seq Data
GEO Series GSE54631. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Identification of a multi-potent Twist2-expressing cell population in the adult heart (single cell RNA-seq data set)
GEO Series GSE118410. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Identification of genetic modifiers of vEDS mice using whole-genome SNP data
GEO Series GSE277421. Mus musculus. 234 samples. Type: Genome variation profiling by SNP array.
Supplemental data for "Using multiple signatures to improve accuracy of substorm identification"
<ul> <li>ace_swepam_2005016.txt: Solar wind data from the SWEPAM instrument of the ACE spacecraft (covering a gap in the published Level 2 dataset)</li> <li>imf_jan2005_merged.dat: Solar wind input to SWMF covering the month of January, 2005</li> <li>dataset_s1.h5: HDF5 file containing substorm onset lists for January, 2005</li> </ul>
FIG. 7 in The genus Navicordulia Machado & Costa, 1995 (Insecta, Odonata, Corduliidae s.str.): new species, identification key for males and data on ecology and distribution
FIG. 7. — Rock-bottomed stream near locus typicus, Barruol Mounts. Photo by Stéphane Brûlé.
Primary data for "Identification of molecular quantum states using phase-sensitive forces"
<p>Figure4_v3.m is a Matlab file that creates Figure4 of the manuscript. It uses auxiliary functions to calculate the polarizability of N2+.</p> <p>Table_I_v3.m is a Matlab file that crates Table I of the manuscript. It uses same auxiliary functions as the last script.</p> <p>RawData.pdf gives the Rabi signals from which the data points in Figure 4 are calculated.</p> <p>CalibrationProcedure.pdf gives additional information on the calibration made using Ca+.</p>
Flesh ID: raw sequence data of the identification of meat source
<p>The data set represent the Fastq sequence files obtained from oxford Nanopore sequencing run of sample contain DNA of nine animal species extracted from meat samples (Horse, Chicken, Turkey, Cattle, Sheep, Duck, Rabbit, Goat and Donkey). </p>
Data from: A reliable DNA barcode reference library for the identification of the European shelf fish fauna
Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based on K2P genetic distances formed nonoverlapping clusters for all species with a ≥99% bootstrap support each. Identification was successful for 100% of the species as the minimum genetic distance to the nearest neighbour always exceeded the maximum intraspecific distance. A barcoding gap was apparent for the whole data set. Within-species distances ranged from 0 to 2.35%, while interspecific distances varied between 3.15 and 28.09%. Distances between congeners were on average 51-fold higher than those within species. The validation of the sequence library by applying BOLDs barcode index number (BIN) analysis tool and a ranking system demonstrated high taxonomic reliability of the DNA barcodes for 85% of the investigated fish species. Thus, the sequence library presented here can be confidently used as a benchmark for identification of at least two-thirds of the typical fish species recorded for the North Sea.
Data from: The identification of loci for immune traitsin chickens using a genome-wide association study
The genetic improvement of disease resistance in poultry continues to be a challenge. To identify candidate genes and loci responsible for these traits, genome-wide association studies using the chicken 60k high density single nucleotide polymorphism (SNP) array for six immune traits, total serum immunoglobulin Y (IgY) level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against Avian Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed. RT-qPCR was used to quantify the relative expression of the identified candidate genes. Nine significantly associated SNPs (P < 2.81E-06) and 30 SNPs reaching the suggestively significant level (P < 5.62E-05) were identified. Five of the 10 SNPs that were suggestively associated with the antibody response to SRBC were located within or close to previously reported QTL regions. Fifteen SNPs reached a suggestive significance level for AIV antibody titer and seven were found on the sex chromosome Z. Seven suggestive markers involving five different SNPs were identified for the numbers of heterophils and lymphocytes, and the heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16, were significantly associated with serum total IgY concentration, and the five most significant were located within a narrow region spanning 6.4kb to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this region, changes in IL4I1, CD1b transcripts were consistent with the concentrations of IgY, while abundances of TRIM27 and ZNF692 showed reciprocal changes to those of IgY concentrations. This study has revealed 39 SNPs associated with six immune traits (total serum IgY level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against AIV and SRBC) in Beijing-You chickens. The narrow region spanning 247kb on chromosome 16 is an important QTL for serum total IgY concentration. Five candidate genes related to IgY level validated here are novel and may play critical roles in the modulation of immune responses. Potentially useful candidate SNPs for marker-assisted selection for disease resistance are identified. It is highly likely that these candidate genes play roles in various aspects of the immune response in chickens.
Data from: Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to non-invasive sampling
Species identification through non-invasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Non-invasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining while several others are poorly studied. Here we develop a genetic tool for identifying all rodent species in Iberia by non-invasive genetic sampling. To achieve this purpose we selected one mitochondrial gene (cytochrome b – cyt-b) and one nuclear gene (interphotoreceptor retinoid-binding protein – IRBP), which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and M. duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to non-invasive samples, we selected a short highly-diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from non-invasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation.
Data from: Identification of children with anaphylaxis at low risk of receiving acute inpatient therapies
Objective: Opportunity exists to reduce unnecessary hospitalizations for children with anaphylaxis given wide variation in admission rates across U.S. emergency departments (EDs). We sought to identify children hospitalized with anaphylaxis at low risk of receiving epinephrine and other acute inpatient therapies, as these patients may be candidates for ED discharge rather than inpatient hospitalization. Methods: We conducted a single-center retrospective cohort study of children 1–21 years of age hospitalized with anaphylaxis from 2009 to 2016. Acute inpatient therapies included intramuscular (IM) or racemic epinephrine, bronchodilators, fluid boluses, vasopressors, non-invasive ventilation, or intubation. We derived age-specific (pre-verbal [<36 months] vs. verbal [≥ 36 months]) prediction rules using recursive partitioning to identify children at low risk of receiving acute inpatient therapies. Results: During the study period 665 children were hospitalized for anaphylaxis, of whom 108 (16.2%) received acute inpatient therapies. The prediction rule for patients < 36 months (no wheezing, no cardiac involvement [hypotension or wide pulse pressure]) had a sensitivity of 90.5% (CI 69.6–98.8%) and a negative predictive value of 98.3% (CI 94.1–99.8%) for identifying children at low risk of receipt of acute inpatient therapies during hospitalization. For children ≥ 36 months, the prediction rule (no wheezing, no cardiac involvement, presence of gastrointestinal symptoms) had a sensitivity of 90.8% (CI 82.7–96.0%) and a negative predictive value of 92.4% (CI 85.6–96.7%). Conclusions: We derived age specific prediction rules for children hospitalized with anaphylaxis at low risk of receiving epinephrine and other acute inpatient therapies. These children may be candidates for ED discharge rather than inpatient hospitalization.
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.
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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.