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Smaller stature in childhood following assisted reproductive technologies (ART) is not explained by parental or gestational factors, early childhood environment, or fetal DNA methylation [GUSTO_buffy_coat]

ABSTRACT: As part of an investigation on contributors to offspring size following assisted reproduction, we investigated maternal mid-/late-pregnancy peripheral blood buffy coat DNA methylation at 240 CpGs previously associated with maternal pregnancy morbidity or offspring growth across various tissues. Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles in previously frozen buffy coat samples from 70 women who conceived via assisted reproduction technologies and gave live births and 845 women who spotaneously conceived and gave live births.

ORGANISM(S): Homo sapiens

PROVIDER: GSE158063 | GEO | 2020/09/16

REPOSITORIES: GEO

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Smaller stature in childhood following assisted reproductive technologies (ART) is not explained by parental or gestational factors, early childhood environment, or fetal DNA methylation [GUSTO_cord_tissue]

Project description:As part of an investigation on contributors to offspring size following assisted reproduction, we investigated fetal cord tissue DNA methylation at 281 CpGs previously associated with maternal pregnancy morbidity or offspring growth across various tissues. The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles in previously frozen cord tissues samples from 69 assisted reproduction-conceived and 950 spotaneously conceived live births.

2020-09-15 | GSE157896 | GEO

Single cell RNAseq reveal covid19 patient immune response

Project description:Eighteen patients admitted to CSMC and diagnosed with COVID19 by RT-PCR were stratified into COVID19 mild/moderate, severe, and recovery groups (n=5-6/group). Venous blood was collected into EDTA coated tubes and centrifuged to separate plasma and buffy coat. Plasma was collected and frozen at -80C, and the buffy coat was collected into cryo-preservation media and frozen at -80C. Recovered cells are sorted for live-dead staining, then fixed with methanol. Fixed single cells were further captured using 10x chromium Next GEM 3 prime v3.1 kit. Two patients samples from the same group were mixed, captured and sequenced together.

2020-09-24 | GSE154567 | GEO

Higher Incidence of Embryonic Defects in Mouse Offspring Conceived with Assisted Reproduction from Fathers with Sperm Epimutations

Project description:Assisted reproductive technologies (ART) account for 1-6% of live births in developed countries. While most children conceived using ART are healthy, increases in birth and genomic imprinting defects have been reported; such abnormal outcomes have been attributed to underlying parental infertility and/or the ART used. Here, we assessed whether paternal genetic and lifestyle factors, that are associated with male infertility and affect the sperm epigenome, can influence ART outcomes. We examined how paternal factors, Dnmt3L haploinsufficiency and/or diet-induced obesity, in combination with ART (superovulation, in vitro fertilization, embryo culture and embryo transfer), could adversely influence embryo development and DNA methylation patterning in mice. While male mice fed high-fat diets (HFD) gained weight and showed perturbed metabolic health, their sperm DNA methylation was minimally affected by the diet. In contrast, Dnmt3L haploinsufficiency induced a marked loss of DNA methylation in sperm; notably, regions affected were associated with neurodevelopmental pathways and enriched in young retrotransposons, sequences that can have functional consequences in the next generation. Following ART, placental imprinted gene methylation and growth parameters were impacted by one or both paternal factors. For the embryos conceived by natural conception, the abnormality rates were similar for WT and Dnmt3L+/- fathers. In contrast, paternal Dnmt3L+/- genotype, as compared to WT fathers, resulted in a 3-fold increase in the incidence of morphological abnormalities in embryos generated by ART. Together, the results indicate that embryonic morphological and epigenetic defects associated with ART may be exacerbated in offspring conceived by fathers with sperm epimutations.

2023-12-05 | GSE234855 | GEO

Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation

Project description:Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells by generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. To evaluate differences in cell composition and DNA methylation between buffy coat and whole cord blood samples, cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in 8 individuals, each contributing buffy coat and whole blood samples.

2018-01-01 | GSE103189 | GEO

Downregulation of micro RNAs 145-3p and 145-5p is a Long-Term Predictor of Postmenopausal Breast Cancer Risk: the ORDET prospective study

Project description:microRNA expression profile of buffy coat derived from healty woman before the insorgence of breast cancer microRNA expression was evaluated from total RNA extracted from buffy coat.

2014-09-10 | E-GEOD-54470 | biostudies-arrayexpress

Downregulation of micro RNAs 145-3p and 145-5p is a Long-Term Predictor of Postmenopausal Breast Cancer Risk: the ORDET prospective study

Project description:microRNA expression profile of buffy coat derived from healty woman before the insorgence of breast cancer

2014-09-10 | GSE54470 | GEO

Epigenome-wide Association study of individuals conceived by Assisted Reproduction Technologies at birth and adulthood

Project description:Epigenome-wide Association study of individuals conceived by Assisted Reproduction Technologies at birth and adulthood

| PRJNA543534 | ENA

Human buffy coat gene expression, custom 250-plex Nanostring panel

Project description:Buffy coat PBMC RNA expression was tested using a custom Nanostring probe panel, to identify general immune and glucocorticoid receptor-associated immune genes. ClinicalTrials.gov Identifier: NCT00824941

2019-11-01 | GSE124549 | GEO

Integrated Analysis of Hub Genes and MicroRNAs in Human Placental Tissues from In Vitro Fertilization-Embryo Transfer [RNA-seq]

Project description:Next generation sequencing was perfomed to identify differentially expressed gene in Placental tissue samples from IVF-ET assisted or natural conceived pregnancies

2021-10-21 | GSE186147 | GEO

Integrated Analysis of Hub Genes and MicroRNAs in Human Placental Tissues from In Vitro Fertilization-Embryo Transfer [miRNA-seq]

Project description:Next generation sequencing was perfomed to identify differentially expressed micro-RNA in Placental tissue samples from IVF-ET assisted or natural conceived pregnancies

2021-10-21 | GSE186148 | GEO

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