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Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]

ABSTRACT: Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]

PROVIDER: PRJNA434675 | ENA |

REPOSITORIES: ENA

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Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]

Project description:Preterm or small for gestational age (SGA) infants are to be at high risk of noncommunicable diseases in adolescence, because they are exposed to hypoxia and malnutrition in and ex utero during perinatal period. Epigenetics could be one of the most important mechanisms of DOHaD.In the field of premature babies, previous studies investigated the methylation alterations related to gestational age and birthweight by using cord blood samples. In the field of preterm or SGA babies, there were few EWAS studies that examine whether methylation changes relate to RNA expression using cord blood samples, and the interpretation of postnatal blood methylation were different by studies.The objective is to investigate the epigenetic alterations associated with preterm birth and SGA by using methylation and expression microarray, and to explore the epigenetic changes which may persist after birth.

2021-02-09 | GSE110828 | GEO

Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [expression]

2021-02-09 | GSE110822 | GEO

Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period

Project description:Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period

| PRJNA434671 | ENA

Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [expression]

Project description:Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [expression]

| PRJNA434653 | ENA

Genomics of the ovine heart ontogeny during the perinatal period

Project description:The period of development from the last two weeks of gestation through the first two weeks of life spans a period of great functional and metabolic challenge to the fetal and neonatal lamb heart. Important changes in gene expression occur to meet these challenges. On this study, septa from sheep hearts at 130 days gestation (n=6), term (n=8, gestational lenght is around 145 days) and 14-days-old lambs (n=8) were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays. Weighted gene co-expression network analysis (WGCNA) determined five major patterns of co-expressed and functionally related genes during this critical period of cardiac transition. Septum samples from the heart were collected from non-treated fetuses at 130 days of gestational age (GA130d, n=6) and term (n=8); and from naturally born 14-days-old lambs (Lamb, n=8). None of the ewes suffered gestational diseases or showed signs of impending labor.

2015-07-30 | E-GEOD-66725 | biostudies-arrayexpress

Genomics of the ovine heart ontogeny during the perinatal period

2015-07-30 | GSE66725 | GEO

Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-02-09 | GSE110829 | GEO

Determining gestational age using genome methylation profile

Project description:Background: Gestational age determination by traditional tools (last menstrual period, ultrasonography measurements and Ballard Maturational Assessment in newborns) have major limitations and therefore there is a need to find molecular marker approaches that can be used to determine the accurate gestational age of the newborn. Methods: We performed RRBS (Reduced Representation Bisulfite Sequencing) on 41 cord blood and matching placenta samples. Results: We identified a set of 316 Differentially Methylated Regions (DMRs) that undergo demethylation in late gestational age in cord blood cells and can predict the gestational age (r = -0.7, p value<0.0001). Once the set of 411 DMRs that undergo de novo methylation in late gestational age was used in combination with the first set it generated a more accurate clock (r=0.77, p value=1.87E-05). Conclusion: Taken together, this study demonstrates that DNA methylation can accurately predict gestational age. The clinical use of this predictor should be further investigated.

2019-07-18 | GSE109538 | GEO

Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period

Project description:Pro-spermatogonia (SG) serve as the gateway to spermatogenesis. Using single-cell RNA sequencing (RNAseq), we studied the development of ProSG, their SG descendants, and testicular somatic cells, during the perinatal period in mice. We identified both gene and protein markers for 3 temporally distinct ProSG cell subsets, including a migratory cell population with a distinct transcriptome from the previously defined T1- and T2-ProSG stages. This intermediate (I)-ProSG subset translocates from the center of seminiferous tubules to the spermatogonial stem cell (SSC) “niche” in its periphery soon after birth. We identified 3 undifferentiated SG subsets at postnatal day 7, each of which express distinct genes, including transcription factor and signaling genes. Two of these subsets have the characteristics of newly emergent SSCs. We also molecularly defined the development of Sertoli, Leydig, and peritubular myoid cells during the perinatal period, allowing us to identify candidate signaling pathways acting between somatic and germ cells in a stage-specific manner during the perinatal period. Our study provides a rich resource for those investigating testicular germ and somatic cell developmental during the perinatal period.

2020-01-22 | GSE130593 | GEO

Global transcriptional profiles of abdominal skin epidermis during perinatal period

Project description:We report global transcriptional alteration and transcriptional heterogeneity of epidermal cells in remodeling mouse abdominal skin during perinatal period. By RNA-sequencing of FACS-isolated interfollicular epidermal (IFE) basal cells from abdominal skin of wildtype (WT) non-pregnant (NP) mice, pregnant mice, and Tbx3 cKO pregnant mice, we revealed pregnancy-associated genes and a key role of Tbx3 in regulating the pregnancy-associated transcriptome. To resolve the transcriptional heterogeneity of epidermal cells at single cell resolution, we performed single cell RNA sequencing of epidermal cells isolated from the abdominal skin of NP mice, pregnant mice, and post-partum mice by using Tbx3creERT2;R26H2B-EGFP mice. By unsupervised evaluation of clustering-based cell identities of total samples on the Seurat platform, we identified 14 main clusters, where the IFE1 cluster was appeared to be enriched in Dpc16 samples, and further revealed the pseudotime differentiation of Tbx3cre labeled cells during perinatal period.

2021-02-17 | GSE136747 | GEO

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