DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE23311 | GEO | 2010/07/31
SECONDARY ACCESSION(S): PRJNA131193
REPOSITORIES: GEO
Similar Datasets
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
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.
2010-08-27 | GSE23835 | GEO
Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples.
2015-03-31 | GSE66210 | GEO
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
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
Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples. Bisulphite converted DNA from the 54 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.
2015-03-31 | E-GEOD-66210 | biostudies-arrayexpress
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
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 Experiment Overall Design: case-control comparisons
2008-11-29 | E-GEOD-12767 | biostudies-arrayexpress
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
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