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2,785 results for “genotyping”
Syngnathus floridae morphometrics and genotyping data
<p>This is the raw data that corresponds to the manuscript "Sexual selection on non-ornamental traits is underpinned by evidence of genetic constraints on sex-biased expression in dusky pipefish" (DOI: <a href="https://doi.org/10.1111/mec.17550">https://doi.org/10.1111/mec.17550</a>). The three .csv datasets contain morphometric data and raw fitness data for all male and female individuals involved in the experiment and the .zip folder contains raw sequencing data.</p> <ol> <li><strong>all_fem_meso_floridae</strong>: contains raw meaures of the different morphometric traits (length, depth, etc.), info about the trial, and collection date/location for all individual female pipefish.</li> <li><strong>all_mal_meso_floridae</strong>: contains raw measures of the different morphometric traits, info about the trial, collection date/location, and pregnancy status for all individual male pipefish.</li> <li><strong>EmbryoParentage</strong>: contains the raw male/female fitness data for all pregnant pipefish. Each row represents a section of a male's pouch and contains information about who the confirmed mother was for each of the genotyped embryos and the total number of developed and undeveloped embryos in that section.</li> <li><strong>genotyping_raw_sequences</strong>: this is a folder that contains all of the raw genotyping files that correspong to all females, males, and embryos from the successful trials. Within the folder is a subfolder for each trial that contains the indivual .fsa for each pipefish adult or embryo.</li> </ol>
Data from: Cost effective microsatellite isolation and genotyping by high throughput sequencing
High throughput sequencing (HTS) has emerged as a valuable tool for the rapid isolation of genetic markers for population genetics and pedigree analysis. HTS-based SNP (single nucleotide polymorphism) genotyping protocols like RAD (Restriction-site associated DNA) sequencing or hybrid capture, allow for the isolation of thousands of markers from any non-model organism. However, these protocols are relatively laborious and expensive and the resulting high marker density is not always necessary. Since HTS technology has also greatly simplified the isolation and genotyping process of microsatellite markers, we develop microsatellite markers as a cost efficient and simple alternative to SNP genotyping. We present low coverage genome sequencing data from seven distantly related spider species (Argiope bruennichi, Larinia jeskovi, Oedothorax restusus, Pisaura mirabilis, Australomisidia ergandros, Cheiracanthium punctorium, Theridion grallator) and show the utility of HTS for microsatellite isolation. We also present a simple Illumina amplicon sequencing protocol to genotype microsatellites from multiplex PCR amplicons in the Hawaiian happy face spider T. grallator. We discuss advantages and drawbacks of the use of microsatellites for a range of research questions, and highlight an unexpectedly fast decay and gain of repeat loci for T. grallator.
Data from: The effects of genotype × phenotype interactions on transcriptional response to silver nanoparticle toxicity in organotypic cultures of murine tracheal epithelial cells
The airway epithelium is critical for maintaining innate and adaptive immune responses, and occupational exposures that disrupt its immune homeostasis may initiate and amplify airway inflammation. In our previous study, we demonstrated that silver nanoparticles (AgNP), which are engineered nanomaterials used in multiple applications but primarily in the manufacturing of many antimicrobial products, induce toxicity in organotypic cultures derived from murine tracheal epithelial cells (MTEC), and those differentiated toward a "Type 2 [T2]-Skewed" phenotype experienced an increased sensitivity to AgNP toxicity, suggesting that asthmatics could be a sensitive population to AgNP exposures in occupational settings. However, the mechanistic basis for this genotype × phenotype interaction (G×P) has yet to be defined. In the present study, we conducted transcriptional profiling using RNA-sequencing (RNA-seq) to predict the enrichment of specific canonical pathways and upstream transcriptional regulators to assist in defining a mechanistic basis for G×P effects on AgNP toxicity. Organotypic cultures were derived from MTEC across two genetically inbred mouse strains (A/J and C57BL/6J mice), two phenotypes ("Normal" and "T2-Skewed"), and one AgNP exposure (an acute 24 h exposure) to characterize G×P effects on transcriptional response to AgNP toxicity. The "T2-Skewed" phenotype was marked by increased pro-inflammatory T17 responses to AgNP toxicity, which are significant predictors of neutrophilic/difficult-to-control asthma and suggests that asthmatics could be a sensitive population to AgNP exposures in occupational settings. This study highlights the importance of considering G×P effects when identifying these sensitive populations, whose underlying genetics or diseases could directly modify their response to AgNP exposures.
Kimberley Fish microsatellite genotypes
<ol> <li>Dispersal is a critically important process that dictates population persistence, gene flow and evolutionary potential and is an essential element for identifying species conservation risks. This project aims to investigate the contributions of dispersal syndromes and hydrographic barriers on patterns of population connectivity and genetic structure in fishes occupying the particularly rugged and fragmented landscape of the Kimberley Plateau, Western Australia.</li> <li>We assessed population genetic structure between three neighbouring catchments (the Mitchell, King Edward and Drysdale rivers) in three congeneric groups of freshwater fishes that exhibit varied dispersal syndromes within and among groups: (1) <i>Melanotaenia australis</i> and <i>M. gracilis</i>; (2) <i>Syncomistes trigonicus </i>and <i>S. rastellus</i>; (3) <i>Hephaestus jenkinsi</i> and <i>H. epirrhinos</i>. Within each species we sampled the upper, middle and lower reaches of each catchment and assessed patterns of gene flow between and within catchments using microsatellite markers.</li> <li>Our results suggest that contemporary connectivity between catchments is greatly limited or absent in all study species, regardless of their dispersal syndromes. However, gene flow within catchments varied in line with predicted dispersal potential with poor dispersers exhibiting limited gene flow and significant genetic structuring.</li> <li>We conclude that the rugged landscape and historical habitat isolation has contributed to patterns of population fragmentation among fish populations from different river catchments. However, it appears dispersal syndromes influence connectivity and gene flow within catchments, where landscape constraints are not as pervasive.</li> <li>This study presents a comparative population genetic analysis of freshwater fishes with differing dispersal syndromes and colonisation ability. Our findings provide new insights into factors shaping patterns of biodiversity on the Kimberley Plateau, and the evolutionary uniqueness of fish communities from different river catchments draining the plateau. The results from this study provide a framework for informing the management of the region's unique freshwater biodiversity.</li> </ol>
Clinical Care of Autosomal Polycystic Kidney Disease: Retrospective Analysis and Prospective PKD Genotyping
ClinicalTrials.gov study NCT02161068. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Trial of Genotype-based Warfarin Initiation in Patients With Mechanical Prosthetic Heart Valve
ClinicalTrials.gov study NCT01633957. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Study of Hepatitis C Virus (HCV) Polymerase Inhibitor Pro-Drug in Combination With PEGASYS With or Without COPEGUS in Patients With Chronic Hepatitis C (CHC) Genotype 1 Infection.
ClinicalTrials.gov study NCT00377182. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Prospective Analysis of "Genotype-phenotype" Correlations Observed in a Large Cohort of Patients With Hereditary Retinal Dystrophies - GEPHIRD
ClinicalTrials.gov study NCT03662386. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Does 3 Months Therapy With Vitamin D + Peg + Ribavirin Improve Sustained Virologic Response (SVR) in Genotype 2, 3 Chronic Hepatitis C Patients?
ClinicalTrials.gov study NCT01151397. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Pilot Study of Genotypic Analysis
ClinicalTrials.gov study NCT00421837. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Establish the PK of Belinostat in Patients With Wild-type, Heterozygous, and Homozygous UGT1A1*28 Genotypes
ClinicalTrials.gov study NCT02680795. IPD Sharing: NO. Countries: 1. Publications: 0.
Kinetics of Fluvoxamine and Digoxin in Subjects With Different MDR1 Genotypes
ClinicalTrials.gov study NCT01704638. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Prevention of Cervical Cancer Using the Genotyping Screening and Same-day Self-sampling
ClinicalTrials.gov study NCT07232355. IPD Sharing: YES. Countries: 3. Publications: 0.
Chronically-infected HCV Genotype 2 and 3 Treatment-naive Subjects: Part A: Safety and Efficacy of INX-08189 With Peg IFN Alfa-2a and Ribavirin. Part B: INX-08189 in Interferon Free Treatment With Dac
ClinicalTrials.gov study NCT01425970. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Sofosbuvir/Ledipasvir for Hepatitis C Genotype 1-6 in Patients With Transfusion-Dependent Thalassemia: An Open Label Trial
ClinicalTrials.gov study NCT03032666. IPD Sharing: NO. Countries: 1. Publications: 0.
SPECT Imaging of DAT Genotype
ClinicalTrials.gov study NCT01492322. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genotype-driven Phase I Study of Irinotecan Administered in Neoadjuvant Chemoradiotherapy in Patients With Stage II/III Rectal Cancer
ClinicalTrials.gov study NCT01474187. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genotype-guided Treatment in Newly Diagnosed PTCL
ClinicalTrials.gov study NCT05675813. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Study of BMS-824393 in Combination With Peginterferon Alfa-2a (Pegasys) and Ribavirin (Copegus) in Treatment Naive Subjects With Chronic Hepatitis C Virus Genotype I
ClinicalTrials.gov study NCT01142700. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Observational Study of Patients With Chronic Hepatitis C Virus (HCV) Infected With HCV Genotype 1 Low Virus Load (LVL 1) and Effect of PegIntron Plus Rebetol Treatment (Study P04793 Part 2)
ClinicalTrials.gov study NCT01054742. IPD Sharing: Not stated. Countries: 0. Publications: 0.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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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.