MMelMel3, paternal haplotype
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ABSTRACT:
PROVIDER: PRJEB49353 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Meles meles (European badger) genome assembly, mMelMel3, maternal haplotype, uncurated
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Project description:Meles meles (European badger), genomic and transcriptomic data
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Project description:Objectives: To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). Methods: DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) genotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. The paternity testing parameters were attributed to each case quantitatively. Results: The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699-99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. Conclusions: Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.
2021-10-25 | GSE186434 | GEO
Project description:Development of the early embryo is thought to be mainly driven by maternal gene products and post-transcriptional gene regulation. Here, we used metabolic labeling to show that RNA can be transferred by sperm into the embryo. To identify genes with paternal expression in the embryo, we performed crosses of males and females from divergent C. elegans strains. RNA sequencing of mRNAs and small RNAs in the 1-cell hybrid embryo revealed that about two hundred paternal mRNAs are reproducibly expressed in the embryo, and that about half of assayed endogenous siRNAs and piRNAs are also of paternal origin. Together, our results suggest an unexplored paternal contribution to early development. To reveal the identity of paternal RNA molecules, we performed a cross of males and females from two divergent C. elegans strains because we reasoned that sequencing of embryonic RNA and SNP analysis should then identify and quantify maternal and paternal transcripts. These sequencing experiments were carried out in purified hybrid 1-cell embryos and comprised small RNAs and mRNAs. For comparison we sequenced mRNAs and small RNAs from the parental strains: paternal (Hawaiian males, CB4856) and maternal (fem-1(hc17ts)/TX189(OMA-1::GFP). For the annotation of strain specific mutations (SNPs) we sequenced mRNA and small RNAs extracted from whole worms. All experiments were performed in at least two independent biological replicates.
2014-06-04 | E-GEOD-57351 | biostudies-arrayexpress
Project description:Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.
2022-11-15 | GSE192501 | GEO
Project description:Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.
2022-11-15 | GSE192499 | GEO