Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Revealing de novo Age-related Genetic Alterations in Mouse Oocytes through Single-cell Exome Sequencing

ABSTRACT: In our study, scWES was employed on oocytes from female mice with different reproductive ages. We also performed whole exome sequencing on bluk blood samples in trios to detect de novo germline variations in oocytes. Both natural aging and accelerated reproductive aging were involved. We demonstrated that genetic alterations, including base variants and structural variations, occurred in mouse oocytes during aging. Genes harboring natural aging or accelerated aging-related de novo germline variants (DNGVs) were almost involved in Ugt1a, V2R, and Mucin gene families. A copy number variant (CNV) associated with chromatin modeling were detected in natural aging oocytes. More importantly, we shortlisted various critical biological functions, like calcium binding pathway and p53 pathways, affected by these aging-related genetic alterations. Our work is the first study to identify genetic alterations in mouse oocytes with in vivo aging and offers a new direction of dissecting the aging mechanisms in oocytes and clarifying genetic causes of lower fertility at advanced maternal age.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus Musculus

SUBMITTER: School of Biomedical Sciences, The Chinese University of Hong Kong

PROVIDER: PRJEB28344 | EVA | 2019-08-01

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Similar Datasets

Project description:Revealing de novo Age-related Genetic Alterations in Mouse Oocytes through Single-cell Exome Sequencing

| PRJEB28344 | ENA

De novo copy number variations in cloned dogs (Illumina SNP)

Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background.

2013-12-17 | GSE49123 | GEO

De novo copy number variations in cloned dogs (Nimblegen)

2013-12-17 | GSE49092 | GEO

De novo copy number variations in cloned dogs (Nimblegen)

2013-12-17 | E-GEOD-49092 | biostudies-arrayexpress

De novo copy number variations in cloned dogs (Illumina SNP)

2013-12-17 | E-GEOD-49123 | biostudies-arrayexpress

Genome-wide Genotyping of Acute Myeloid Leukemia with Translocation t(9;11)(p22;q23) Reveals Novel Recurrent Genomic Alterations

Project description:To identify cooperating lesions in de novo and therapy-related acute myeloid leukemia (t-AML) with translocation t(9;11)(p22;q23) we performed high-resolution SNP-array profiling on 40 leukemia samples [de novo: n=22; t-AML: n=16; unknown: n=2]. A mean of 1.73 copy number alterations (CNAs)/case were identified with no differences between de novo and t-AML cases. We identified a novel minimally deleted region (MDR) at 7q36.1-q36.2 partly overlapping with a MDR previously identified in core-binding factor AML; MLL3 was the only gene affected in both regions. In addition, a recurrent gain was found at 13q21.33-q22.1 harboring the potential oncogene KLF5. Sequence/expression analysis of selected candidate genes revealed deregulated EVI1 at high frequency (50%). Copy-neutral loss-of-heterozygosity (CN-LOH) was absent in the paired cohort Further analysis of the candidate genes might provide novel insights into the pathogenesis of t(9;11) AML SNP genotyping was performed on 40 de novo and therapy-related MLL-MLLT3-rearranged acute myeloid leukemia samples; Germline control DNA from remission bone marrow or peripheral blood was available for paired analysis in 15 patients. Data were processed using reference alignment, dChipSNP and circular binary segmentation.

2014-05-22 | E-GEOD-46745 | biostudies-arrayexpress

NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing

Project description:While de novo DNA methylation (DNAme) in mammalian germ cells is dependent upon DNMT3A and DNMT3L, oocytes and spermatozoa show distinct patterns of DNAme. In mouse oocytes, de novo DNAme requires the lysine methyltransferase (KMTase) SETD2, which deposits H3K36me3. Surprisingly, we show here that SETD2 is dispensable for de novo DNAme in the male germline. Rather, the KMTase NSD1, which broadly deposits H3K36me2 in euchromatic regions, plays a critical role in de novo DNAme in prospermatogonia, including of imprinted genes. However, males deficient in germline NSD1 show a more severe defect in spermatogenesis than Dnmt3l-/- males. Furthermore, unlike DNMT3L, NSD1 safeguards a subset of genes against H3K27me3-associated transcriptional silencing. In contrast, H3K36me2 plays only a minor role in de novo DNAme during oogenesis and females with NSD1 deficient oocytes are fertile. Thus, the sexually dimorphic pattern of DNAme in mature mouse gametes is driven by distinct profiles of H3K36 methylation.

2020-07-10 | GSE148150 | GEO

Clinically Relevant Copy Number Variations Detected in Cerebral Palsy

Project description:Cerebral palsy (CP) represents a group of non-progressive clinically heterogeneous disorders that are characterized by motor impairment and early age-of-onset, frequently accompanied by co-morbidities. The cause of CP has historically been attributed to environmental stressors resulting in brain damage. While genetic risk factors are also implicated, guidelines for diagnostic assessment of CP do not recommend for routine genetic testing. Given numerous reports of etiologic copy number variations (CNVs) in other neurodevelopmental disorders, we used microarrays to genotype a population-based prospective cohort of children with CP and their parents. Here we identify de novo CNVs in 8/115 (7.0%) CP patients (~1% rate in controls). In four children, large chromosomal abnormalities deemed pathogenic were found, and they were significantly more likely to have severe neuro-motor impairments than those CP subjects without such alterations. Overall the CNV data would have impacted our diagnosis or classification of CP in 11/115 (9.6%) families. Dr. Maryam Oskoui* , Mr. Matthew Gazzellone* , Ms. Bhooma Thiruvahindrapuram , Dr. Mehdi Zarrei , Dr. John Andersen , Dr. John Wei , Dr. Zhouzhi Wang , Dr. Richard Wintle , Dr. Christian Marshall , Dr. Ronald Cohn , Dr. Rosanna Weksberg , Dr. James Stavropoulos , Dr. Darcy Fehlings , Dr. Michael Shevell, Dr. Stephen Scherer. Clinically Relevant Copy Number Variations Detected in Cerebral Palsy. Nature Communications, 2015. Following our rigorous quality control procedure, we successfully genotyped 147 proband samples from individuals with cerebral palsy (81 males and 66 females) and 282 samples obtained from parents (134 males and 148 females). This facilitated the identification of de novo and rare inherited copy number variations of clinical interest.

2015-07-28 | E-GEOD-70374 | biostudies-arrayexpress

Transformation of the Fallopian Tube Secretory Epithelium Leads to High-grade Serous Ovarian Cancer in BRCA/P53/PTEN Models

Project description:Our study presents the first genetic models of de novo high-grade serous carcinomas (HGSC) that originate in fallopian tube secretory epithelial cells and recapitulate the key genetic alterations and precursor lesions characteristic of human invasive ovarian cancer. Genomic copy number analysis, using array CGH, was performed on murine tumors in order to compare the overlap of copy number alterations between HGSC models and TCGA data. Array CGH was performed on genomic DNA isolated from murine HGSC tumors. Genomic DNA from three normal mouse fallopian tubes was pooled and used as the reference.

2013-12-17 | E-GEOD-49827 | biostudies-arrayexpress

Mutations in the SHANK2 synaptic scaffolding gene in autism spectrum disorder and mental retardation

Project description:Autism spectrum disorder (ASD) and mental retardation (MR) represent clinically distinct neurodevelopmental disorders with a complex genetic etiology. Using microarrays we identified de novo copy number variations in the SHANK2 synaptic scaffolding gene in two unrelated ASD and MR patients; DNA sequencing of SHANK2 revealed additional variants including a de novo nonsense mutation and 7 rare inherited changes. Our findings further link common genes between ASD and intellectual disability.

2010-05-01 | GSE20533 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data