Quality control measures for placental sample purity in DNA methylation array analyses
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ABSTRACT:
PROVIDER: PRJNA545414 | ENA |
REPOSITORIES: ENA
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Project description:The purity of tissue samples can affect the accuracy and utility of DNA methylation array analyses. This is particularly important for the placenta which is hypomethylated. Placental villous tissue from early pregnancy terminations can be difficult to separate from the non-villous tissue, resulting in potentially inaccurate results. We used several methods to identify mixed placental samples using DNA methylation array datasets from our laboratory and those contained in the NCBI GEO database, highlighting the importance of determining sample purity during quality control processes.
2020-06-09 | GSE131945 | GEO
Project description:The purity of tissue samples can affect the accuracy and utility of DNA methylation array analyses. This is particularly important for the placenta which is globally hypomethylated compared to other tissues. Placental villous tissue from early pregnancy terminations can be difficult to separate from non-villous tissue, resulting in potentially inaccurate results. We used several methods to identify mixed placenta samples using DNA methylation array datasets from our laboratory and those contained in the NCBI GEO database, highlighting the importance of determining sample purity during quality control processes.
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Project description:Nicotine is a common environmental pollution which is diffused into the air in the form of cigarette smoke fumes. Due to its lipophilic nature, nicotine can rapidly transport through membrane barriers and spread throughout the body which leads to abnormalities in the human brain, heart and even the fatal. However, the effects of nicotine on early embryonic development remains elusive. In this study, we found that nicotine significantly affected early embryonic development with decreased blastocyst formation. In addition, embryos treated with nicotine caused increased level of ROS, DNA damage and cell apoptosis. By RNA sequencing analysis, we demonstrated that nicotine affected the expression of placental development genes. Consistently, we found that the placental development at E17.5 was impaired by nicotine exposure, with increased placental weight and disrupted placental structure. This was due to excessive activation of the Notch signaling pathway, since blocking Notch signal by DAPT treatment recovered abnormal placental weight and structure induced by nicotine exposure. We also observed that nicotine exposure could specifically cause promoter hypermethylation of Phlda2 (a maternally expressed imprinted gene associated with placental development) and lead to its abnormal expression. Overall, this study provides evidence that nicotine causes the declining quality of early embryo and leads to placental abnormalities related with over-activation of the Notch signaling pathway.
2023-10-17 | GSE186660 | GEO
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Project description:We used human + mouse cell mixtures to demonstrate the purity of PIP-seq single cell RNA-sequencing
2023-01-12 | GSE202911 | GEO
Project description:The placenta mediates adverse pregnancy outcomes, including preeclampsia, characterized by gestational hypertension and proteinuria. Placental cell type heterogeneity in preeclampsia is not well-understood and limits mechanistic interpretation of bulk gene expression measures. We generated single-cell RNA-sequencing samples for integration with existing data to create the largest deconvolution reference of 19 fetal and 8 maternal cell types from placental villous tissue at term. We deconvoluted eight published microarray case-control studies of preeclampsia. Our findings indicate substantial placental cellular heterogeneity in preeclampsia that predict previously observed bulk gene expression differences. Our deconvolution reference lays the groundwork for cellular heterogeneity-aware investigation into placental dysfunction and adverse birth outcomes.
2022-08-22 | GSE182381 | GEO
Project description:Host cell proteins (HCPs) are process-related impurities generated during biotherapeutic protein production. HCPs can be problematic if they pose a significant metabolic demand, degrade product quality, or contaminate the final product. Here, we present an effort to create a “clean” Chinese hamster ovary (CHO) cell by disrupting multiple genes to eliminate HCPs. Using a model of CHO cell protein secretion, we predicted the elimination of unnecessary HCPs could have a non-negligible impact on protein production. We analyzed the total HCP content of 6-protein, 11-protein, and 14-protein knockout clones and characterized their growth in shake flasks and bioreactors. These cell lines exhibited a substantial reduction in total HCP content (40%-70%). We also observed higher productivity and improved growth characteristics, in specific clones. With the reduced HCP content, protein A and ion exchange chromatography more efficiently purified a monoclonal antibody (mAb) produced in these cells during a three-step purification process. Thus, substantial improvements can be made in protein titer and purity through large-scale HCP deletion, providing an avenue to increased quality and affordability of high-value biopharmaceuticals.
2020-03-19 | GSE144624 | GEO
Project description:The goal of our experiment is to compare the cytokines and membrane factors that are differentially expressed between akt-activated endothelial cells and mesenchymal progenitors. Those two cell type have previously been described as potential niche for HSC expansion in vivo and in vitro. We isolated placental mesenchymal progenitors as previously described (Raynaud CM. et al. 2012 stem cell international). HUVECs cells were also isolated from cord and transfected with E4ORF1 as previously described (Seandel M. et al. 2008 PNAS). Both cell type were grown separately 3 days in X-Vivo media complemented with TPO, Flt3 and SCF (HSc amplification media). Pl-MPs and E4+ECs RNA was isolated using Trizol reagent followed by additional purification using RNAeasy extraction kit from Qiagen (74106, QIAGEN) with RNA yields that produces satisfactory microarray data. Two quality control measures were carried out: (1) A spectrophotometric analysis (2) A size fractionation procedure using a microfluidics instrument (Agilent Technologies). 200 ng of total RNA were analyzed on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Data were analyzed using Parteck Software (V6.09.1110-6; Affimetrix).
2013-08-30 | E-MEXP-3725 | biostudies-arrayexpress