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Dataset results
29 results for “molecular genotyping”
Fig. 2 in New genotypes and molecular characterization of Enterocytozoon bieneusi in pet birds in Southwestern China
Fig. 2. Phylogenetic tree based on the internal transcribed spacer (ITS) sequences obtained in this study in relation to published sequences from GenBank using ML methods. Enterocytozoon bieneusi genotypes identified in the present study are indicated in bold-type, and genotypes PtEbIX (DQ85585) and CD8 (KJ668735) from dogs were used as outgroups.
Fig. 1 in New genotypes and molecular characterization of Enterocytozoon bieneusi in pet birds in Southwestern China
Fig. 1. Sequence variation in the ITS region of the rRNA gene of Enterocytozoon bieneusi isolates from pet birds. The ITS sequences of five known genotypes (D, SC02, BEB6, CHB1, and MJ5) and the three novel genotypes (SCB-I, SCB-II, and SCB-III), identified in this study, were aligned with each other.
Fig. 1. Phylogenetic relationship among the Enterocytozoon bieneusi groups. The relationship between the E in New genotypes and molecular characterization of Enterocytozoon bieneusi in captive black bears in China
Fig. 1. Phylogenetic relationship among the Enterocytozoon bieneusi groups. The relationship between the E. bieneusi genotypes identified in this study and other known genotypes deposited in GenBank was inferred by neighbor-joining analysis of ITS sequences based on genetic distance using the Kimura-2-parameter model. The numbers on the branches represent percent bootstrapping values from 1000 replicates, with more than 50% shown in the tree. Each sequence is identified by its accession number, genotype designation, and host origin. Genotypes marked with black rhombuses and black triangles are novel and known genotypes identified in this study, respectively.
Fig. 1. Phylogenetic relationships between the E in Molecular characterization and novel genotypes of Enterocytozoon bieneusi in pet snakes in Beijing, China
Fig. 1. Phylogenetic relationships between the E. bieneusi genotypes identified in this study and other reported genotypes. The relationships were inferred using maximum likelihood analysis of the ITS rRNA gene and the values generated greater than 70% are shown beside the nodes. Genotypes with filled circles and triangles are known and novel genotypes identified in this study, respectively.
Fig. 1 in Molecular detection and genotypes of Enterocytozoon bieneusi in farmed mink (Neovison vison), blue foxes (Alopex lagopus), and raccoon dogs (Nyctereutes procyonoides) in Xinjiang, China
Fig. 1. Phylogenetic relationships of the E. bieneusi genotypes. The relationships were inferred using NJ analysis of the ITS rRNA gene and the values generated greater than 50% are shown beside the nodes. Genotypes with hollow circles and filled circles are known and novel genotypes identified in this study, respectively.
Fig. 1 in Molecular detection and characterization of a novel Theileria genotype in Dama Gazelle (Nanger dama)
Fig. 1. Phylogenetic analyses of sequence data for 393bp 18S rRNA gene of Theileria spp. in gazelles by Maximum Likelihood method with bootstrap of 1000 replications using MEGA software version10.
Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease
<p>Leaf scald caused by the bacteria <em>Xanthomonas albilineans</em> is one of the major concerns to sugarcane production. To breed for resistance, mechanisms underlying plant-pathogen interaction need deeper investigations. Herein, we evaluated sugarcane defense responses against <em>X. albilineans</em> using molecular and biochemical approaches to assess pathogen-triggered ROS, phytohormones and metabolomics in two contrasting sugarcane genotypes from 0.5-144 h post-inoculation (hpi). In addition, the infection process was monitored using TaqMan-based quantification of <em>X. albilineans</em> and the disease symptoms were evaluated in both genotypes after 15 d post-inoculation (dpi) The susceptible genotype presented a response to the infection at 0.5 hpi, accumulating defense-related metabolites such as phenolics and flavonoids with no significant defense responses thereafter, resulting in typical symptoms of leaf scald at 15 dpi. The resistant genotype did not respond to the infection at 0.5 hpi but constitutively presented higher levels of salicylic acid and of the same metabolites induced by the infection in the susceptible genotype. Moreover, two subsequent pathogen-induced metabolic responses at 12 and 144 hpi were observed only in the resistant genotype in terms of amino acids, quinic acids, coumarins, polyamines, flavonoids, phenolics and phenylpropanoids together with an increase of hydrogen peroxide, ROS-related genes expression, indole-3-acetic-acid and salicylic acid. Multilevel approaches revealed that constitutive chemical composition and metabolic reprogramming hampers the development of leaf scald at 48 and 72 hpi, reducing the disease symptoms in the resistant genotype at 15 dpi. Phenylpropanoid pathway is suggested as a strong candidate marker for breeding sugarcane resistant to leaf scald.</p>
Fig. 2 in Molecular detection and characterization of a novel Theileria genotype in Dama Gazelle (Nanger dama)
Fig. 2. The clade credibility values of phylogram generated from bayesian analysis.
Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology
Minimally-invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally-invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction-site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally-invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.
The Role of the Tumor Molecular Profile (CMS), UGT1A1 Genotype and Beta-glucuronidase Activity of the Intestinal Microbiota for Treatment Efficiency, Toxicity, Survival and Quality of Life in Patients
ClinicalTrials.gov study NCT05655780. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: A new multiplex SNP genotyping assay for detecting hybridization and introgression between the M and S molecular forms of Anopheles gambiae
Open the record for dataset details and reuse information.
Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology
Open the record for dataset details and reuse information.
A genotype-first approach for the molecular and clinical characterization of uncommon de novo microdeletion of 20q13.33
GEO Series GSE21536. Homo sapiens. 6 samples. Type: Expression profiling by genome tiling array; Genome variation profiling by SNP array.
Prostate cancer stratification using molecular profiles [CamCap genotype first set]
GEO Series GSE71965. Homo sapiens. 300 samples. Type: Genome variation profiling by SNP array.
Prostate cancer stratification using molecular profiles [CamCap genotype third set]
GEO Series GSE73012. Homo sapiens. 7 samples. Type: Genome variation profiling by SNP array.
Reproduction-associated and sex determining genes expressed differently in testes of genotypic and temperature-induced males of gibel carp (Carassius gibelio): the molecular mechanisms underlying the
GEO Series GSE285878. Carassius gibelio. 26 samples. Type: Expression profiling by high throughput sequencing.
Time of day and genotype sensitivity adjust molecular responses to temperature stress in Sorghum
GEO Series GSE225632. Sorghum bicolor. 96 samples. Type: Expression profiling by high throughput sequencing.
Prostate cancer stratification using molecular profiles [Stockholm genotype]
GEO Series GSE73076. Homo sapiens. 180 samples. Type: Genome variation profiling by SNP array.
Transcriptional profiling in Finger millet (Eleusine coracana) genotypes provides insights into the molecular basis of salinity tolerance in tolerant genotype.
GEO Series GSE55462. Eleusine coracana. 4 samples. Type: Expression profiling by high throughput sequencing.
Prostate cancer stratification using molecular profiles [CamCap genotype second set]
GEO Series GSE73011. Homo sapiens. 28 samples. Type: Genome variation profiling by SNP array.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.