Similar Datasets
Project description:Effect of chemicals in ES cell differentiation
| PRJNA511393 | ENA
Project description:This study provides a comprehensive evaluation of changes in gene expression during treatment with environmental chemicals in embryonic bodies derived from mouse embryonic stem (ES) cells. ES cells were maintained under the feeder cells in phenol red-free DMEM Medium (supplemented with 15% FBS, 100uM Non-essential amino acids (NEAA), 1000U/ml Leukemia inhibitory factor(LIF), 100uM 2-mercaptoethanol(2-ME), and 0.5% penicillin/streptomycin). Cells were gently washed in warm PBS and transferred to phenol red-free DMEM Medium (supplemented with 15% KnockOut Serum Replacement, 100uM NEAA, 100uM 2-ME, and 0.5% penicillin/streptomycin) in Microsphere array (MSA300F) and exposed with low and high levels of each chemical just after removing LIF from the culture media. Prior to collection, cells were washed in warm PBS, resuspended and briefly incubated in the QIAGEN RLT buffer, and finally collected in triplicate at 48 hours. Following RNA isolation, the best RNA yields for each replicate set was selected for target preparation and microarray processing.
2009-10-10 | GSE18503 | GEO
Project description:To develop molecular indicators of neurodevelopmental disorders related to the exposure to external chemicals, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to influence neuronal differentiation from embryonic stem cells. Thalidomide (TMD), bisphenol A (BPA), 4-hydroxy-2,2',3,4',5,5',6-heptachlorobiphenyl (4OH-PCB187) and 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) were exposed to human embryonic stem (ES) cell-derived sphere on day 3 after starting sphere formation for 72 hours. Gene expression analysis on the stage of sphere development showed chemical specific characteristics.
2020-05-28 | GSE151239 | GEO
Project description:We performed an untargeted metabolomic analysis on surficial human skin samples collected with moistened cotton swabs (water: ethanol, 50:50) using LC-HR-MS/MS. Data-dependent Acquisition was employed under positive ionization mode. Two cohorts were included, subjects exposed and non-exposed to petroleum-based chemicals.
2020-10-21 | MSV000086350 | MassIVE
Project description:Sall4 is a transcription factor essential for early mammalian development. Though it is reported to play an important role in embryonic stem (ES) cell self-renewal, whether it is an essential pluripotency factor has been disputed. Though Sall4 is known to associate with the Nucleosome Remodeling and Deacetylase (NuRD) complex, the nature of this interaction is unclear as NuRD and Sall4 serve opposing functions in ES cells. Here we use defined culture conditions and single-cell gene expression analyses to show that Sall4 prevents activation of the neural gene expression programme in ES cells but is dispensable for maintaining the pluripotency gene regulatory network. We further show using genome-wide analyses that while Sall4 interacts with NuRD, it neither recruits NuRD to chromatin nor influences transcription via NuRD. Rather we propose a model where, by titrating Sall4 protein, NuRD limits the differentiation-inhibiting activity of Sall4 in ES cells to enable lineage commitment.
2016-08-02 | PXD003614 | Pride
Project description:We chronically exposed HepaRG (differentiated hepatic cells that retain primary human hepatocytes characteristics) and HepaG2 (liver hepatocarcinoma cells) liver cells to physiologically relevant concentrations of Cadmiun and PFOAs chemicals (10nM) to observed how these affect global gene expression in these cellular models.
2022-05-15 | E-MTAB-11670 | biostudies-arrayexpress
Project description:Gene expression profiles of mouse ES cells (D0) and neural precusor cells (D6)
2009-11-04 | GSE18772 | GEO
Project description:The excitement and controversy surrounding the potential role of human embryonic stem (ES) cells in transplantation therapy have often overshadowed their potentially more important use as a basic research tool for understanding the development and function of human tissues. Human ES cells can proliferate without a known limit and can form advanced derivatives of all three embryonic germ layers. What is less widely appreciated is that human ES cells can also form the extra-embryonic tissues that differentiate from the embryo before gastrulation. The use of human ES cells to derive early human trophoblast is particularly valuable, because it is difficult to obtain from other sources and is significantly different from mouse trophoblast. Here we show that bone morphogenetic protein 4 (BMP4), a member of the transforming growth factor-beta (TGF-beta) superfamily, induces the differentiation of human ES cells to trophoblast. DNA microarray, RT-PCR, and immunoassay analyses demonstrate that the differentiated cells express a range of trophoblast markers and secrete placental hormones. When plated at low density, the BMP4-treated cells form syncytia that express chorionic gonadotrophin (CG). These results underscore fundamental differences between human and mouse ES cells, which differentiate poorly, if at all, to trophoblast. Human ES cells thus provide a tool for studying the differentiation and function of early human trophoblast and could provide a new understanding of some of the earliest differentiation events of human postimplantation development. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-11-04 | GSE3553 | GEO
Project description:Various chemicals, including pesticides, heavy metals, and metabolites of tobacco, have been detected in fetal environment. Fetuses are exposed to these chemicals at relatively low concentrations; however, their risk of developing neurological and behavioral disorders increases after birth. We aimed to evaluate the effects of five chemicals (diethylphosphate, cotinine, octachlorodipropyl ether, mercury, and selenium) detected in the serum of pregnant mothers on DNA methylation status during neural development using human neural stem cells.
2023-12-06 | GSE235146 | GEO
Project description:TET-family enzymes convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. Tet1 and Tet2 are Oct4-regulated enzymes that together sustain 5hmC in mouse embryonic stem (ES) cells. ES cells depleted of Tet1 by RNAi show diminished expression of the Nodal antagonist Lefty1, and display hyperactive Nodal signalling and skewed differentiation into the endoderm-mesoderm lineage in embryoid bodies in vitro. In Fgf4- and heparin-supplemented culture conditions that favor derivation of trophoblast stem (TS) cells, Tet1-depleted ES cells activate the trophoblast stem cell lineage determinant Elf5 and can colonize the placenta in mid-gestation embryo chimeras. Consistent with these findings, Tet1-depleted ES cells form aggressive hemorrhagic teratomas with increased endoderm, reduced neuroectoderm and ectopic appearance of trophoblastic giant cells. Thus Tet1 functions to regulate the lineage differentiation potential of ES cells. Here, we performed whole-genome transcriptome profiling of ES cells stably depleted of Tet1 by shRNA knockdown (Tet1-kd) cultured in either standard ES cell or in TS cell culture conditions. Gene expression changes in Tet1-kd ES cells were fairly modest compared to control (GFP-kd) cells, although gene ontology (GO) analysis of differentially expressed genes yielded many terms related to embryonic development and cell cycle regulation. In TS cell culture conditions, a core set of genes defining trophectodermal cell differentiation, including Cdx2, Eomes and Tead4, was enriched in Tet1-kd compared to GFP-kd cells.
2011-02-07 | GSE26900 | GEO