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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of human chorionic villus samples from preeclampsia patients

ABSTRACT: 4 chorionic villus sampling specimens in pregnancies destined for preeclampsia and 8 matched controls were analyzed; 36 genes were differentially expressed using J5 score and prediction modeling in caGEDA computer program Experiment Overall Design: case-control comparisons

ORGANISM(S): Homo sapiens

SUBMITTER: Sandra Anne Founds

PROVIDER: E-GEOD-12767 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Altered global gene expression in first trimester placentas of women destined to develop preeclampsia.

Founds S A SA Conley Y P YP Lyons-Weiler J F JF Jeyabalan A A Hogge W Allen WA Conrad K P KP

Placenta 20081121 1

<h4>Background</h4>Preeclampsia is a pregnancy-specific disorder that remains a leading cause of maternal, fetal and neonatal morbidity and mortality, and is associated with risk for future cardiovascular disease. There are no reliable predictors, specific preventative measures or treatments other than delivery. A widely held view is that the antecedents of preeclampsia lie with impaired placentation in early pregnancy. Accordingly, we hypothesized dysregulation of global gene expression in firs ...[more]

PMID: 19027158

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Chorionic villus sampling (CVS) microarray in preeclampsia

Project description:4 chorionic villus sampling specimens in pregnancies destined for preeclampsia and 8 matched controls were analyzed 36 genes were differentially expressed using J5 score and prediction modeling in caGEDA computer program Keywords: snap frozen, banked CVS specimens with known pregnancy outcomes revealed genes differentially expressed in preeclampsia pregnancies

2008-11-25 | GSE12767 | GEO

DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells

Project description:Comparative analysis of DNA methylation in 12 human chorionic villus samples and 12 human maternal blood cell samples We performed a genome wide analysis of DNA methylation first trimester CVS samples and gestational age matched MBCs. We analyzed DNA samples obtained from 12 CVS samples and 12 MBC samples. Data were generated using two high-throughput approaches: the Infinium “humanmethylation27” platform marketed by Illumina and a custom Agilent-based platform. We then compared these data with genome wide transcription data for the same tissues. This Series covers only the Illumina HumanMethylation27 part of the study.

2010-07-31 | E-GEOD-23311 | biostudies-arrayexpress

DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells

Project description:Comparative analysis of DNA methylation in 12 human chorionic villus samples and 12 human maternal blood cell samples

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Human chorionic villus proteome

Project description:We evaluated the effect of the different solubilization techniques on the reproducibility and width of the chorionic proteome characterized using bottom-up proteomics: SDS-based solubilization coupled with in-gel protein digestion after applying self-named 1DE gel-concentration procedure (SDS-PAGE without fractionating in the resolving gel for SDS removal) and in-solution protein digestion of urea-thiourea extracts. These results indicated that 1DE-concentration procedure coupled with in-gel digestion, LC-MS/MS and combinational usage of different bioinformatics tools provides in-depth analysis of a single protein band, including reliable identification and quantification of low-abundant proteins, e.g. FUCA1, PSG7.

2022-06-17 | PXD024759 | Pride

DNA Methylation Predictors of Gene Expression in the 1st Trimester Chorionic Villus: Implications for Prenatal Diagnosis

Project description:Placental gene expression is a finely controlled process, yet little is known about the factors that regulate it, including epigenetic factors such as DNA methylation. In this study, we quantified the effects of DNA methylation on placental gene expression. Using targeted high throughput sequencing, we generated methylation profiles of 3.7 million CpG dinucleotides from 6 karyotypically normal CVS samples and compared these to gene expression data obtained from a publically available database. We found a broad association between methylation and gene expression at both the chromosome and individual gene levels. At the chromosome level, we found alternating domains of high and low methylation. Within each gene, we found distinct methylation patterns at different regulatory genetic elements. For example, the promoters of highly expressed genes were neither highly methylated, nor completely unmethylated. Rather, they had < 50% of the CG dinucleotides in their sequences in the methylated state. In contrast, promoters of unexpressed genes tended to be either highly methylated or fully unmethylated. Similarly, patterns of methylation in exons and introns differed between highly expressed and unexpressed genes. Our data show that the relationship between DNA methylation and gene expression is nuanced: highly expressed and unexpressed genes differ, not only by their extent of methylation, but also by minute changes in the locations of their methylation sites. DNA methylation analysis of placental genes may help predict abnormal placental gene expression and pregnancy complications, making it a possible tool for prenatal diagnosis. DNA from 6 chorionic villus samples from the 1st trimester (from 3 male and 3 female fetuses) as well as 3 maternal blood cell samples was extracted, hybridized to probes in the Agilent SureSelectXT Methyl-Seq Target Enrichment kit, targeting 84Mb of the genome and then bisulfite converted before sequencing.

2016-06-25 | E-GEOD-58826 | biostudies-arrayexpress

Analysis of transcriptional differences after IFN-beta (IFN-b) or IFN-lambda (IFN-l) treated human mid-gestation chorionic villus explants

Project description:Purpose: Treatment of midgestation chorionic villus explants with recombinant IFN-b leads to morphological changes including formation of syncitial knots. However, treatment of explants with IFN-l, which is constitutively expressed by syncytiotrophoblasts, is not sufficient to cause these same changes. To understand the different transcriptional changes induced by IFN-b and IFN-l and underlying cause of these morphological changes, we performed RNAsequencing after these different treatments. Methods: Chorionic villi of 18-21 gestation week placentas were dissected. Explants were cultured in DMEM F/12 with 1000 U recombinant IFN-b or 1000U recombinant IFN-l for 24 hours. RNA was then isolated from explants, and RNAsequencing was performed to assess transcriptional changes. Results/ Conclusions: IFN-b but not IFN-l induces interferon stimulated genes (ISGs) in mid gestation chorionic villus explants.

2017-12-31 | GSE104348 | GEO

DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells Using Custom Agilent CGH Arrays

Project description:We present a detailed structural and functional analysis of the placental epigenome at its maternal interface. Specifically, we analyzed the DNA methylation pattern of chromsomes 13, 18, and 21 in samples of chorionic villus (CVS) and maternal blood cells (MBC) using custom designed microarrays. We then compared these data with transcription data for the same tissues. In addition to the discovery that CVS genomes are significantly more hypomethylated than their MBC counterparts, we identified numerous tissue-specific differentially methylated regions (T-DMRs). We further discovered that these T-DMRs are clustered spatially along the genome and are enriched for genes with tissue-specific biological functions. We identified unique patterns of DNA methylation associated with distinct genomic structures such as gene bodies, promoters and CpG islands and identified both direct and inverse relationships between DNA methylation levels and gene expression levels in gene bodies and promoters respectively. Furthermore, we found that these relationships were significantly associated with CpG content. We conclude that the early gestational placental DNA methylome is highly organized and is significantly associated with transcription. These data provide a unique insight into the structural and regulatory characteristics of the placental epigenome at its maternal interface and will drive future analyses of the role of placental dysfunction in gestational disease. Two-condition experiment, CVS vs. MBC cells. Biological replicates: 2 pooled CVS samples, 2 pooled MBC samples, collected from different patients. Each sample is divided into two parts, one part treated with HpaII enzyme, one part without. The two parts then are hybridized to the two channels of the same array. Two arrays for each sample, with dye swap to remove dye bias.

2010-08-27 | E-GEOD-23835 | biostudies-arrayexpress

RNA-seq of first-trimester chorionic villus for understanding the maintenance of early gestation as well as pathogenesis in pregnancy-related disorders

Project description:Implant failure and insufficient placental development are important causes of female infertility, recurrent miscarriage, and other pregnancy-related problems. A better understanding of gene expression profiling based on high-throughput sequencing technology is important for the study on the development of the placenta and the causes of pregnancy-related diseases. In this study, we collected 6 first-trimester chorionic villus and decidua tissues and obtained the transcriptome database on high-throughput sequencing. We performed routine principal component analysis (PCA) on these 12 samples and identified differentially expressed genes from samples with different sex background. And identified genes highly expressed in villus and decidua, respectively.

2019-08-31 | E-MTAB-8186 | biostudies-arrayexpress

DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells Using Custom Agilent CGH Arrays

2010-08-27 | GSE23835 | GEO

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