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Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE209816 | GEO | 2023/06/08

REPOSITORIES: GEO

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Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

2023-06-08 | GSE209815 | GEO

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [ATAC-seq]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

2023-06-08 | GSE209810 | GEO

Characterization of a strain-specific CD-1 reference genome reveals potential inter- and intra-strain functional variability.

Project description:BackgroundCD-1 is an outbred mouse stock that is frequently used in toxicology, pharmacology, and fundamental biomedical research. Although inbred strains are typically better suited for such studies due to minimal genetic variability, outbred stocks confer practical advantages over inbred strains, such as improved breeding performance and low cost. Knowledge of the full genetic variability of CD-1 would make it more useful in toxicology, pharmacology, and fundamental biomedical research.ResultsWe performed deep genomic DNA sequencing of CD-1 mice and used the data to identify genome-wide SNPs, indels, and germline transposable elements relative to the mm10 reference genome. We used multiple genome-wide sequencing data types and previously published CD-1 SNPs to validate our called variants. We used the called variants to construct a strain-specific CD-1 reference genome, which we show can improve mappability and reduce experimental biases from genome-wide sequencing data derived from CD-1 mice. Based on previously published ChIP-seq and ATAC-seq data, we find evidence that genetic variation between CD-1 mice can lead to alterations in transcription factor binding. We also identified a number of variants in the coding region of genes which could have effects on translation of genes.ConclusionsWe have identified millions of previously unidentified CD-1 variants with the potential to confound studies involving CD-1. We used the identified variants to construct a CD-1-specific reference genome, which can improve accuracy and reduce bias when aligning genomics data derived from CD-1 mice.

| S-EPMC10401811 | biostudies-literature

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

| PRJNA862518 | ENA

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]

| PRJNA862520 | ENA

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [ATAC-seq]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [ATAC-seq]

| PRJNA862524 | ENA

Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies.

Project description:BackgroundThe microsatellite, (GATA)n has been frequently used for DNA fingerprinting. However, very few attempts have been made to analyze (GATA)n-containing loci in rice.ResultsThree polymorphic (GATA)n-harboring loci viz. OS1A6, OS1H10 and OS2E7, containing 7-13 repeat motifs were identified from a genomic library of a cultivated rice, Oryza sativa var. Basmati-370 using oligonucleotide probe (GATA)4. When (GATA)n flanking primers were used to screen 26 wilds (representing different genomes of rice), 16 cultivars, 47 Indian elite rice varieties and 37 lines resistant/susceptible to bacterial blight, up to 22 alleles were obtained at an individual locus. Also, interestingly the bacterial blight resistant lines clustered into a separate group from the remaining rice genotypes, when a dendrogram was constructed based on the polymorphism obtained at the three loci. This may be due to the partial homology of the clones OS1H10 and OS2E7 to regions encoding O. longistaminata receptor kinase-like protein and pathogenesis-related protein. The ability of these O. sativa flanking primers to amplify DNA of maize, wheat, barley and oat indicates that these (GATA)n-containing loci are conserved across different cereal genera.ConclusionsThe large allele number obtained reveals the potential of (GATA)n-containing loci as powerful tools to detect simple sequence length polymorphism (SSLP). The (GATA)n-flanking primers were not only useful in distinguishing between closely related genotypes, but could also be used for cross-species amplification and are also conserved across different cereal genera. These loci could also cluster the bacterial blight resistant/susceptible lines into different groups based on the resistance genes present in them.

| S-EPMC59831 | biostudies-literature

The community structure of functional brain networks exhibits scale-specific patterns of inter- and intra-subject variability.

Project description:The network organization of the human brain varies across individuals, changes with development and aging, and differs in disease. Discovering the major dimensions along which this variability is displayed remains a central goal of both neuroscience and clinical medicine. Such efforts can be usefully framed within the context of the brain's modular network organization, which can be assessed quantitatively using computational techniques and extended for the purposes of multi-scale analysis, dimensionality reduction, and biomarker generation. Although the concept of modularity and its utility in describing brain network organization is clear, principled methods for comparing multi-scale communities across individuals and time are surprisingly lacking. Here, we present a method that uses multi-layer networks to simultaneously discover the modular structure of many subjects at once. This method builds upon the well-known multi-layer modularity maximization technique, and provides a viable and principled tool for studying differences in network communities across individuals and within individuals across time. We test this method on two datasets and identify consistent patterns of inter-subject community variability, demonstrating that this variability - which would be undetectable using past approaches - is associated with measures of cognitive performance. In general, the multi-layer, multi-subject framework proposed here represents an advance over current approaches by straighforwardly mapping community assignments across subjects and holds promise for future investigations of inter-subject community variation in clinical populations or as a result of task constraints.

| S-EPMC7734597 | biostudies-literature

Ocean warming and acidification adjust inter- and intra-specific variability in the functional trait expression of polar invertebrates.

Project description:Climate change is known to affect the distribution and composition of species, but concomitant alterations to functionally important aspects of behaviour and species-environment relations are poorly constrained. Here, we examine the ecosystem ramifications of changes in sediment-dwelling invertebrate bioturbation behaviour-a key process mediating nutrient cycling-associated with near-future environmental conditions (+ 1.5 °C, 550 ppm [pCO2]) for species from polar regions experiencing rapid rates of climate change. We find that responses to warming and acidification vary between species and lead to a reduction in intra-specific variability in behavioural trait expression that adjusts the magnitude and direction of nutrient concentrations. Our analyses also indicate that species behaviour is not predetermined, but can be dependent on local variations in environmental history that set population capacities for phenotypic plasticity. We provide evidence that certain, but subtle, aspects of inter- and intra-specific variation in behavioural trait expression, rather than the presence or proportional representation of species per se, is an important and under-appreciated determinant of benthic biogeochemical responses to climate change. Such changes in species behaviour may act as an early warning for impending ecological transitions associated with progressive climate forcing.

| S-EPMC11217501 | biostudies-literature

Intra and Inter-specific Variability of Salt Tolerance Mechanisms in <i>Diospyros</i> Genus.

Project description:Saline stress is one of most important problems that agriculture must face in the context of climate change. In the Mediterranean basin, one of the regions most affected, persimmon production can be compromised by this effect, due to the limited availability of salt tolerant rootstocks. Seedlings coming from four populations from the Diospyros genus have been exposed to salt stress in order to identify salt tolerance genotypes within these populations. Morphological, physiological, and transcriptomic approaches have revealed different mechanisms of tolerance among the population studied. An HKT1-like gene has been shown to have different root expression related to the salt tolerance phenotypes among and within populations. Additionally, we have observed differences in salt-responsive expression among PIP aquaporin genes. Genetic variability for salt tolerance can be generated in Diospyros species through crossings and used for overcome salt stress. Furthermore, differences in water use efficiency (WUE) have been obtained between and within populations. The information gathered at transcriptomic and physiological level demonstrated natural and heritable variability among Diospyros genus which is the key for salt-tolerant rootstock breeding programs.

| S-EPMC7427203 | biostudies-literature

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