Ontology highlight
ABSTRACT:
PROVIDER: PRJNA504030 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.
2023-06-30 | GSE234146 | GEO
Project description:We report on a genome-wide scan for introgression in the house mouse (Mus musculus domesticus) involving the Algerian mouse (Mus spretus), using 20 samples from the ranges of sympatry and allopatry. Our analysis reveals significant variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the chromosomes in each genome harbor all detectable introgression. Further, a surprising result is that European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we propose three hypotheses. First, at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent. Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, our analysis revealed introgressed genes of functional importance, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature, and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies.
2014-11-01 | GSE62906 | GEO
Project description:By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. Analysing the segregation of the methylation patterns for a subset of these regions shows variations in the penetrance of paramutation-like interactions.
2017-08-18 | GSE97206 | GEO
Project description:Population genomics of emperor penguins using RADseq
| PRJNA384210 | ENA
Project description:Deep sequencing of total RNA extracted from the genital discs of males for each of the following strains : Drosophila sechellia, Drosophila mauritiana, hybrid introgression line 3Q1(A) and hybrid introgression line Q1(A)
2011-07-22 | GSE28663 | GEO