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

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

ORGANISM(S): Mus musculus

PROVIDER: GSE209815 | 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 [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 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

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

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-06-08 | GSE209816 | 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 [ATAC-seq]

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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

Mus musculus strain:CD1

Project description:Mus musculus strain:CD1 Transcriptome or Gene expression

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Widespread inter-individual gene expression variability in Arabidopsis thaliana

Project description:A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability over a 24 hours time-course between individual Arabidopsis thaliana plants growing in stable conditions. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene size, the number of transcription factors regulating a gene and the chromatin environment. These results will bring a new light into the impact of transcriptional variability in gene expression regulation in plants.

2018-12-06 | GSE115583 | GEO

Characterization of CD1- and CD1+ porcine blood dendritic cells confirm them as orthologues of the two major mammalian conventional subsets

Project description:Porcine CD1- and CD1+ dendritic cells represent the orthologues of human and mouse cDC1 and cDC2 cellssubsets respectively

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Epigenome analysis of liver samples from C57BL/6J, CD1, and Sv129Ev mice in lifelong chronic psychosocial stress (LCPS)

Project description:Genome wide DNA methylation profiling of liver tissues from 17 months old male mice belonging to either the C57BL/6J, the CD1 or the Sv129Ev strain and exposed to LCPS. The Illumina Infinium Mouse Methylation Beadchip was used to obtain DNA methylation profiles across approximately 285,000 CpGs in liver samples. Samples included 19 C57Bl/6J mice, 12 CD1 mice, and 16 Sv129Ev mice.

2023-03-31 | GSE216631 | GEO

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