Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification and Characterization of the Epigenome and Transcriptome in Human Neonates

ABSTRACT: We performed reduced-representation bisulfite sequencing (RRBS) on 137 umbilical cord blood (UCB) samples and 158 parental peripheral blood (PPB) samples from nuclear families with either singletons or twins. The samples were classified into five groups based on the mode of conception: spontaneous (CTRL), IVF-ET, IVF-FET, ICSI-ET and ICSI-FET. There were no significant differences in the clinical features of the neonates among the different groups; in addition, maternal ages were under 35 years old and parental body mass index (BMI) values were comparable in general. In addition, we performed chromatin immunoprecipitation sequencing (ChIP-seq) on 33 UCB samples to examine histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) and RNA sequencing (RNA-seq) on 32 UCB samples to examine the transcriptomes of neonates.

ORGANISM(S): Homo sapiens

PROVIDER: GSE136849 | GEO | 2020/08/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide microRNA expression profiling in placentae from frozen-thawed embryo transfer (FET)

Project description:Frozen-thawed embryo transfer (FET) is increasingly available for the improvement of the success rate of assisted reproductive technologies other than fresh embryo transfer (ET). There have been numerous findings that FET provides better obstetric and perinatal outcomes. However, the birth weight of infants conceived using FET is heavier than that of those conceived via ET. In addition, some reports have suggested that FET is associated with perinatal diseases such as placenta accreta and pregnancy-induced hypertension and a decrease in the sex ratio of male infants. These phenotypic alterations are caused by epigenetic alterations. MicroRNAs (miRNAs) are one of epigenetic modifications and dysregulation of miRNAs due to the environment in utero leads to placenta-associated diseases in infants and subsequently chronic diseases later in life. In this study, we compared miRNA expression profiles in the placentas originated from intracytoplasmic sperm injection and FET (ICSI-FET), intracytoplasmic sperm injection and ET (ICSI-ET) and from intracytoplasmic sperm injection and FET (ICSI-FET), intracytoplasmic sperm injection and ET (ICSI-ET) and spontaneous pregnancies (SP).

2017-08-16 | GSE85270 | GEO

Hepatic RNA sequence in male mice offspring conceived by in-vitro Fertilization and Frozen-thawed Embryo Transfer

Project description:Our study reported an increased risk of metabolic disorders in in-vitro Fertilization and Frozen-thawed Embryo Transfer (IVF-FET) conceived offspring compared with those born after IVF-ET. To explore the underlying mechanisms of the aberrant metabolism in male offspring conceived by IVF and FET compared with natural conceived (NC), we performed the RNA-sequencing of livers from three groups. We performed GSEA analysis. The results suggested more severe alterations in the expression of genes involved in insulin resistance pathway in the FET-chow group than that in the IVF-chow group.

2021-01-15 | GSE164819 | GEO

The idiopathic preterm delivery methylation profile in umbilical cord blood

Project description:Genome wide DNA methylation differences in umbilical cord blood (UCB) of preterm and term born neonates. The Illumina 450K Human DNA methylation Beadchip was used to obtain the DNA methylation profiles of 12 preterm and 12 term UCB samples across 450,000 CpGs. 2 samples were removed due to failed quality control, and BMIQ normalization was done with 11 preterm and 11 term samples.

2015-08-17 | GSE66459 | GEO

Umbilical cord blood methylome analysis of IVF neonates that underwent embryo culture in G5 or HTF medium

Project description:Follow-up study of IVF neonates who underwent embryo culture in G5 (Vitrolife) or HTF (Lonza) medium. Genome-wide DNA methylation profiling of IVF neonates (umbilical cord blood samples) who had undergone embryo culture in G5 medium (Vitrolife) or HTF medium (Lonza). The EPIC array was used to profile the methylome at approximately 850,000 CpG sites across the human genome.

2022-05-26 | GSE189531 | GEO

Impact of Assisted Reproduction, Infertility, Sex, and Paternal Factors on the Placental DNA Methylome

Project description:Children conceived using Assisted Reproductive Technologies (ART) have a higher incidence of growth and birth defects, attributable in part to epigenetic perturbations. Both ART and germline defects associated with parental infertility could interfere with epigenetic reprogramming events in germ cells or early embryos. Mouse models indicate that the placenta is more susceptible to the induction of epigenetic abnormalities than the embryo, and thus the placental methylome may provide a sensitive indicator of ‘at risk’ conceptuses. Our goal was to use genome-wide profiling to examine the extent of epigenetic abnormalities in matched placentas from an ART/infertility group and control singleton pregnancies (n=44/group) from a human prospective longitudinal birth cohort, the 3D Study. Principal component analysis revealed a group of ART outliers. The ART outlier group was enriched for females and a subset of placentas showing loss of methylation of several imprinted genes including GNAS, SGCE, KCNQT1OT1 and BLCAP/NNAT. Within the ART group, placentas from pregnancies conceived with IVF/ICSI showed distinct epigenetic profiles as compared to those conceived with less invasive procedures (ovulation induction, intrauterine insemination). Male factor infertility and paternal age further differentiated the IVF/ICSI group, suggesting an interaction of infertility and techniques in perturbing the placental epigenome. Together, the results suggest that the human placenta is sensitive to the induction of epigenetic defects by ART and/or infertility, and we stress the importance of considering both sex and paternal factors and that some but not all ART conceptuses will be susceptible.

2018-10-01 | GSE120250 | GEO

Transcription profiling of human cumulus cells in vitro isolated from polycystic ovary syndrome lean and obese individuals reveals PCOS in lean and obese individuals is associated with different molecular pathways

Project description:Objective: The etiology of PCOS is mostly unknown. Existing data support both genetic and environmental factors in its pathogenesis. Design: Prospective case - control study. Setting: University Hospital. Patients: 25 patients undergoing IVF-ICSI treatment. Intervention: Genome-wide oligonucleotide microarray technology was used to study differential gene-expression patterns of cultured human cumulus cells from IVF patients divided into 4 groups according to disease state (PCOS vs. Control) and BMI (Obese vs. Lean). Results: Two differential PCOS gene expression profiles were established: Lean-Type was formed by comparing PCOS lean (PL) vs. non-PCOS lean (NL) individuals; Obese-Type was formed by comparing PCOS obese (PO) vs. non-PCOS (NO) obese patients. Conclusions: Different molecular pathways are associated with PCOS in Lean and Obese individuals, as demonstrated by gene expression profiling of cumulus cells. Our findings provide insights into the molecular pathogenesis of PCOS. We used microarrays to study the gene expression of human cultured cumulus cells. We compared the genes expression of lean PCOS, Obese PCOS, lean controls and obese controls. Different molecular pathways are associated with PCOS in Lean and Obese patients. Experiment Overall Design: Cumulus cells obtained from woman undergoing IVF/ICSI. Following oocyte retrieval, cumulus cells were stripped from the oocyte, in preparation for the ICSI process, with a micropipette. After 48h in culture the cumulus cells were collected for RNA extraction and hybridization on Affymetrix microarrays. We compered the expression profile of 4 groups - lean PCOS, obese PCOS, lean controls and obese controls.

2008-06-11 | E-GEOD-10946 | biostudies-arrayexpress

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

Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes

Project description:Prenatal exposure to maternal stress and depression has been identified as a risk factor for adverse behavioral and neurodevelopmental outcomes in early childhood. However, the molecular mechanisms through which maternal psychopathology shapes offspring development remain poorly understood. We analyzed transcriptome-wide gene expression profiles of 149 UCB samples from neonates born to mothers with prenatal PTSD (n=20), depression (n=31) and PTSD with comorbid depression (PTSD/Dep; n=13), compared to neonates born to carefully matched trauma exposed controls without meeting PTSD criteria (TE; n=23) and healthy mothers (n=62). We also evaluated physiological and developmental measures in these infants at birth, six months and twenty-four months. A multistep analytic approach was used that specifically sought to: 1) identify dysregulated genes, molecular pathways and discrete groups of co-regulated gene modules in UCB associated with prenatal maternal psychopathologies; and 2) to determine the impact of perinatal PTSD and depression on early childhood development outcomes.

2018-05-25 | GSE114852 | GEO

Study on VEGF regulation mechanism of acupuncture improving endometrial receptivity in IVF-ET

Project description:We find that the Endometrial Blood Vessel Generation is an important part ofthe establishment of Endometrial Receptivity. We have demonstrated inprevious experiments: Acupuncture in IVF-ET treatment can effectively improve Endometrial Receptivity and improve the pregnancy rate, therefore, we proposea VEGF signaling pathway in Acupuncture can improve Endometrial receptivity, thus improving the success rate of IVF-ET Hypothesis. Around the hypothesisintends to adopt the rat model of IVF-ET, through methods of acupuncture, acupuncture combined with blocker, research the related indexes effect performance that acupuncture on the VEGF signaling pathway in endometrial. Using experimental techniques such as Morphological observation, ELIAS, Immunohistochemistry, Real-time quantitative PCR, Methylation-sensitive high-resolution melting curve method(MS-HRM), to complete the research ofobserving the Effect of acupuncture interference IVF-ET, Blocking the impaction VEGF to the effect, the relationship VEGF or gene methylation inits receptors with effect. From the molecular level clarify the adverse effects and mechanism action that acupuncture will improve IVF-ET superovulation of endometrial receptivity, through adjust VEGF signaling pathway, to provide a scientific basis for acupuncture in IVF-ET treatment

2021-12-09 | GSE190472 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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