Effects of antagonist of retinoid X receptor (UVI3003) on morphology and gene profile of Xenopus tropicalis embryos
ABSTRACT: Retinoid X receptor (RXR) plays an important role in the development of vertebrates, and the agonists of RXR are well-known to induce featured malformations in vertebrate embryos. However, there is no information about the teratogenicity of antagonists of RXR in vertebrate embryos. We exposed embryos of amphibian (Xenopus tropicalis) at stages 10/11 to a highly selective antagonist of RXR (UVI3003). The experiments were initiated when embryos reached stage 10/11, the embryos were exposed to 250, 500, 750 µg/L UVI3003 for 0-24 and 24-48 for microarray analysis (n=24).
Project description:Zygotic genome activation (ZGA), which is according to the midblastula transition in zebrafish, is an important event during the maternal-zygotic transition in animals. Our preliminary study and other group’s works indicate that epigenetic regulations play an essential role in ZGA. Morpholino was employed to knockdown PRMT6. We used microarrays to analyze the global gene expression in prmt6 morphants. prmt6 MO (0.3mM) was injected into the one-two cell zebrafish, prmt6 cMO (0.3mM) injection as a control. At 6 hpf, embryos were classified into three subtypes (normal, mild and severe) and prepared for global gene expression analysis with Affymetrix Zebrafish Genome Arrays. The severe subtype and the control were repeated three times.
Project description:The direct conversion, or trans-differentiation, of non-cardiac cells into cardiomyocytes by forced expression of transcription factors and microRNAs provide promising ways of cardiac regeneration. However, genetic manipulations are still not desirable in real clinical applications. we report the generation of automatically beating cardiomyocyte-like cells from mouse fibroblasts with only chemical cocktails. These chemical-induced cardiomyocyte-like cells (CiCMs) express cardiomyocyte-specific markers, exhibit sarcomeric organization, and possess typical cardiac calcium flux and electrophysiological features. Microarray-bassed gene expression patterns of Mouse embryonic fibroblasts (MEFs), CiCMs, and cardiomyocytes(CMs) indicated a clear transition from dividing MEFs to differentiated cardiomyocyte-like state in CiCM samples. Mouse embryonic fibroblasts were treated with a small-molecule combination CRFVPT (10 μM CHIR99021 (C); 10 μM RepSox (R); 50 μM Forskolin (F); 0.5 mM VPA (V); 5 μM Parnate, (P); 1 μM TTNPB (T)) to induce transdifferentiation to chemical-induced cardiomyocyte-like cells. CiCMs beating clusters were picked at day 24 for analysis. MEFs were isolated from mouse embryos, and CMs were isolated from mouse hearts. Total RNA of MEFs, CiCMs and CMs were extracted and hybridization on Affymetrix microarrays.
Project description:Compare difference Global expression profile of hiPSCs between hESCs and human Somatic cells, showing that hiPSCs and hESCs is consistent in lineages and indicated that the induce method is safe and reliable. There are three groups of samples, each group has two repeated samples, hiPSCs respectively compared with hESCs and human Urine-Derived Cells.
Project description:When PDMSCs were induced to heptocytes in vitro, cells mophology, stem cell markers, mitochondrial metabolism will change according to the differentiated status.But dedifferentiation reverses differentiated cells to a more primitive phenotype and PDMSCs will retain the multilineage potency. Furthermore, it will leads to the alteration of gene expression pattern. We used microarrays to detail the global programme of gene expression underlying dedifferentiation and hepatogenic differentiation prcocesses, we intend to identify distinct classes of differentiated genes during these processes. Human PDMSCs at passage 5 were induced to hepatocytes for 11 days, then the inductive medium was replaced by general culture medium for 1 day. Then human PDMSCs, hepatogenic PDMSCs at 11 days, dedifferentiated PDMSCs were selected for RNA extraction and hybridization on Affymetrix microarrays. To that end, we hand-selected cells at three time-points: before hepatogenic induction (P), hepatogenic PDMSCs at 11 days (H) and dedifferentiated PDMSCs for 1 day (DH) .
Project description:Long noncoding RNAs (lncRNAs) have been implicated in the formation of many different types of tumors. However, expression profiles and potential functions of lncRNAs in non-functioning pituitary adenomas (NFPAs) have not been systematically evaluated. We evaluated the expression profiles and potential functions of lncRNAs in non-functioning pituitary adenomas (NFPAs). 10 formalin-fixed and paraffin-embedded (FFPE) tissue specimens (5 non-functioning pituitary adenomas (NFPAs) and 5 normal pituitaries(NPs)) were selected for RNA extraction and hybridization on Affymetrix microarrays. The NFPAs team was designed as the Tumor group (T), while the NPs team was designed as Normal group (N).
Project description:Gliomas arising in the brainstem and thalamus are devastating tumors that are difficult to surgically resect due to their proximity to eloquent brain structures. Here, we performed a comprehesive genomic and epigenomic study, using gene expression and methylation microarrays, to research on th different genomic and epigenetic signatures between brainstem, thalamic, and supratentorial gliomas. Comparison of brainstem, thalamic and supratentorial gliomas
Project description:The high concentration of Well5 cells was resuspended into 20μl PBS, the needle along the tibia direction, before reaching in a breakthrough sense, direct injection cells. At 7 days after injection, proximal tibia was able to reach mass production. At 20 days after injection, the proximal tibia mass increased.If prolonging exposure by BLI,this stage displayedthat tumor cell signalsbegan to lung metastasis. Osteosarcoma orthotopic lung metastasis model was successfully constructed. Total RNA was extracted from sorted osteosarcoma cells of the primary site and lung metastases using Trizol (Invitrogen). We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during osteosarcoma lung metastasis. In support of the notion that fibrosis marks the lung metastasis, the expression of numerous fibrosis-related genes such as FN1, COLs, and MMPs were upregulated from the primary site to lung metastasis in Well5-luc orthotopic inoculation model. Total RNA was extracted from sorted osteosarcoma cells using Trizol (Invitrogen). Gene expression profiling was conducted by Shanghai Biotechnology Corporation using Affymetrix U133 plus 2.0 arrays (Affymetrix, Santa Clara, CA). All data were analyzed according to the manufacturer’s protocol. Raw data generated from Affymetrix CEL files were normalized by RMA background correction; values were log2 transformed. For the enrichment of P values of each GO term, we used Fisher’s exact test to calculate P values and R package stats to calculate FDR (q value) by BH method (www.r-project.org).
Project description:We knocked down EP300 and examined the expression of lncRNA625 target genes. Gene expression profiling of knockdown samples on cDNA microarrays indicated that EP300 affected expression of several lncRNA625 downstream target genes Stably-transfected KYSE150, transfected with shlncRNA625 or shscramble, were collected and lysed in TRIzol (Life technologies). Microarray experiments were performed following the Affymetrix protocol at the Shanghai Biotechnology Corporation.
Project description:To delineate the putative biological functions for lncRNA625, We performed expression profile from stably-transfected KYSE150 transfected with shlncRNA625 or shscramble for functions of lncRNA625 in ESCC Stably-transfected KYSE150, transfected with shlncRNA625 or shscramble, were collected and lysed in TRIzol (Life technologies). Microarray experiments were performed following the Affymetrix protocol at the Shanghai Biotechnology Corporation.
Project description:MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs of about 22 nt in length. Uveal melanoma is the most common intraocular malignant tumor in adults. Our previous result of microarray analysis showed that miR-142-3p was distinctly downregulated in uveal melanoma cells on which miR-142-3p was speculated to have important regulatory effect. In order to better understand the function of miR-142-3p in uveal melanoma and identify its gene targets, we performed transcriptomic microarray analysis. This was done by comparing gene expression profile changes in uveal melanoma cells transfected with miR-142-3p with that transfected with a negative control.