RNA-seq of human HepG2 cells treated with sodium oleate, 17β-estradiol and ER-alpha siRNA
ABSTRACT: HepG2 cells are only treated with 60 μg/ml sodium oleate as group 1, and treated with 60 μg/ml sodium oleate and 50 ng/ml E2 as group 2, and treated with 60 μg/ml sodium oleate, 50 ng/ml E2 and ER-alpha as group 3. All the treatment last for 48 hours and each group have two replications.
Project description:To development of our gene expression, we have employed whole rhesus monkey genome microarray expression profiling as a discovery platform to identify genes with the potential to induce immune response. The peripheral blood from rhesus macaques, who were immunized in groups of three with the capsular polysaccharide (CPS antigen), carrier protein tetanus toxoid (TT) or conjugate vaccine via intramuscular injection (i.m.) in the anterolateral thigh on days 0, 30 and 60 using the formulations, were obtained on days 0, 30, 60 and 90. PBMCs were collected for microarray assays. Dynamic expression variations of eight genes (KLRC1, LGALS13, LTB4DH, NUAK1, VNN2, GALNT3, LOC710050 and LOC716305) were maintained in Hib conjugate vaccine group throughout experiment comparing with the CPS antigen group and carrier protein TT group. Overall design: Hib conjugate vaccine, Hib capsular polysaccharide (CPS) and carrier protein tetanus toxoid (TT) induced gene expression in macaque blood was measured at 0, 30, 60 days after immunized to doses of 0.5 ml. 0.5ml Hib conjugate vaccine contains 10 μg polyribosyl ribitol phosphate (PRP) and 30 μg TT, 0.5 ml Hib capsular polysaccharide (CPS) contains 10 μg PRP, and 0.5 ml carrier protein tetanus toxoid (TT) contains 30 μg TT. Two independent macaques were performed in each group.
Project description:J1 mouse embryonic stem cells (mESCs) and NIH-3T3 fibroblasts were grown in standard media conditions. Hybridized cells were fixed with 4% paraformaldehyde; incubated for 12 hours at 30C in an RNA preserving hybridization (RPH) buffer (300 mM Sodium chloride, 30mM Sodium citrate, 2.1M Ammonium sulfate, 25% formamide, 10 mM EDTA, 1 mg/ml E. Coli tRNA, 500 μg/ml BSA); and reverse cross-linked for 1 hour at 50C in with Sodium dodecyl sulfate (SDS) and Proteinase K (100 mM NaCl, 10 mM pH 8.0 Tris, 1 mM EDTA, 0.5% SDS, 500 μg/ml Proteinase K). one replicate per sample
Project description:Mouse induced pluripotent stem cells (iPSCs) were derived from embryonic fibroblasts by overexpressing the Yamanaka factors Oct4, Sox2, Klf4 and c-Myc, and grown in standard 2i/serum media conditions. Hybridized iPSCs were fixed with 4% paraformaldehyde; incubated for 12 hours at 30C in an RNA preserving hybridization buffer (300 mM Sodium chloride, 30mM Sodium citrate, 2.1M Ammonium sulfate, 25% formamide, 10 mM EDTA, 1 mg/ml E. Coli tRNA, 500 μg/ml BSA); and reverse cross-linked for 1 hour at 50C in with Sodium dodecyl sulfate (SDS) and Proteinase K (100 mM NaCl, 10 mM pH 8.0 Tris, 1 mM EDTA, 0.5% SDS, 500 μg/ml Proteinase K). RNA extracted from live and hybridized iPSCs (1 sample each) was compared by microarray.
Project description:The purpose of this study was to determine which genes are differentially regulated by the E3 ligase Nrdp1 in CD8+ T cells after treatments with anti-CD3/CD28 Abs. The results demonstrate increased induction of cytotoxicity-associated genes in Nrdp1-/- mice than in Nrdp1+/+ mice after activation. Thus Nrdp1 may be involved in the regulation of TCR signaling. Naive CD8+ T cells derived spleens of Nrdp1+/+ and Nrdp1-/- mice were either untreated or treated with immobilized anti-CD3 (5 μg/ml) and soluble anti-CD28 (1 μg/ml) Abs for 4h or 8h. Equal amounts of RNA were assayed for gene expression using Affymetrix mouse 430 2.0 arrays.
Project description:In order to assess the alteration of lncRNA expression in 16HBE cell treated with PM2.5 samples, we determined the lncRNA expression profiles in 16HBE cell treated with PBS (control group) and PM2.5 samples (low dose 125 μg/mL and high dose 500 μg/mL) using lncRNA Microarray. 16HBE Cells were treated with PM2.5 suspension at concentration of 125 μg/mL and 500 μg/mL, and PBS was used in the control group for 48 h. Then, total RNAs were extracted for lncRNA chip preparation and analysis.
Project description:Gene expression profiles of chicken preadipocytes were constructed using Chicken Genome Arrays to determine the gene expression patterns of preadipocytes derived from two chicken lines divergently selected for abdominal fat content. Oleate was used as an inducer of preadipocyte differentiation, and the different expressed genes between the normal and oleate treated preadipocyte were analyzed. Overall design: Cultured preadipocytes were divided into four groups, including the lean line preadipocytes cultured normally (LC), the fat line preadipocytes cultured normally (FC), the lean line preadipocytes treated with oleate (L) and the fat line preadipocytes treated with oleate (F). For the lean and fat chicken lines respectively, the abdominal adipose tissues of 15 male birds with 10 day-old were excised and pooled. The pooled abdominal adipose tissues were digested. Digestion was followed by filtration through a 20um screen and centrifugation at 800 g for 10 min at room temperature. This phase allowed the separation of floating adipocytes from the preadipocytes. The preadipocytes were treated with ACK lysis buffer to remove the red blood cells. The preadipocytes at this stage with a high purity were not cultured and a part of the preadipocytes were collected as the 0001 time point. The remaining preadipocytes were seeded at a density of 5x10^4 cells/cm2 in the medium and maintained at 37°C in a humidified, 5% CO2 atmosphere until confluence (3 to 4 d). The preadipocytes were passaged once and harvested when 50% confluent (named as -12h) and 95% confluent (named as 0h). From the 0h time point, the preadipocytes were divided into two groups. The preadipocytes in one group were treated with 160 ug/ml oleate. The preadipocytes in another group were cultured with normal situation as the control. The preadipocytes from the oleate treated and control groups were collected at 12h, 24h, 72h and 120h.
Project description:Supercritical rosemary extract (containing 16.90% carnosic acid, 1.90% carnosol and 13.59% volatile compounds) showed antitumor activity on colon cancer cells in vitro. We treated colon cancer cells with the extract and we employed whole genome microarray expression profiling to identify genes potentially involved in its antitumor mechanism of action. We analyzed gene expression of colon cancer SW620 cells after treating during 48h with supercritical rosemary extract at concentrations that cause 50% inhibition of cell viability (30 μg/mL), citostatic effect (60 μg/mL) and 50% cell death (100 μg/mL), in comparison to control cells (0 μg/mL). Two independent experiments were performed in triplicate. Each sample is the pool of the triplicates of one of the experiments (a or b) at the indicated concentration.
Project description:We investigated the antifungal mechanism of action (MOA) of compound NSC319726 against C. albicans SC5314. We used transcriptome analysis of wild type C. albicans treated or not with compound. Exponentially growing cells were treated for 60 min with 4 μg/ml of NSC319726. Overall design: Exponentially growing cells were treated for 60 min with 4 μg/ml of NSC319726. The total RNAs were extracted from treated and control cells, then used to synthesize cDNA for microarray assays with Agilent DesignID 037557 that contains 6101 genes in duplicate.
Project description:Responses of Escherichia coli W3110 after treatment with 0.01 M Sodium Azide in Bonner-Vogel medium + 50 ug/ml Tryptophan Keywords: time course Overall design: Escherichia coli W3110 cells sampled at several time points (5, 15, 30, 60 min) after addition of 0.01 M sodium azide in Bonner-Vogel + 50 ug/ml Tryptophan, vs untreated