Treatment of CHRF288-11 Megakaryocytic Cells with Wnt compounds
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ABSTRACT: CHRF288-11 cells were treated with Wnt3a (150ng/ml) and/ot Wnt5a (1200ng/ml) and RNA was harvested after 8 hours of treatment Gene expression was analysed using Human WG6 V3 Illumina Beadarrays There are four experimental groups (Wnt3a Treated, Wnt5a Treated, Wnt3a + Wnt5a treated and Untreated (control)), each with three biological replicates
Project description:In order to investigate the impact of MMP-14 (MT1-MMP) and three-dimensional (3D) culture conditions on the transcriptomes of a human breast adenocarcinoma cell line, we performed a microarray analysis from RNAs isolated from MCF-7 cells expressing either an empty vector (CTRL) or human MMP-14 cDNA (MT1) in monolayer (2D) and 3D collagen (3D Col) growth conditions. MCF-7 cells were stably transfected with either an empty vector (pcDNA3.1/Zeo) or human MMP-14 cDNA (pcDNA3.1-MMP-14/Zeo). Cells were grown for 24, 48 and 72 hours in three-dimensional (3D) type I collagen gels or in monolayer culture conditions. Cells were then lysed in TRIzol and total RNA was isolated. For each experimental condition, total RNAs isolated from 4 independant biological replicates were pooled.
Project description:The ablated Cyp27b1 mice showed no difference in mammary development but tumorigenesis was significantly accelerated. Cell proliferation, angiogenesis, cell cycle progression and survival markers were upregulated by Cyp27b1 ablation, a pattern confirmed by microarray analysis. Triplicate samples each of control mice and Cyp27b1 knockout mice.
Project description:Objective We have previously shown that expression of the CEACAM1 long isoform (CC1-L) in metastatic colorectal cancer (CRC) cells results in significant inhibition of liver metastasis via Chemokine (C-C motif) Ligand 2 (CCL2) and Signal Transducer and Activator of Transcription 3 (STAT3) signaling. Yet, despite recent advances in identifying molecules involved in the CC1-L inhibition of metastasis, much remains to be elucidated regarding the molecular mechanisms orchestrating this pathway. Design We performed an untargeted transcript profiling and a phosphokinase screen between CC1-L-expressing and non-expressing (CT) CRC cells. Identified targets were validated in vitro and in vivo for their involvement in signaling and invasion or metastasis. We validated our conclusions in CRC patient cohorts for time to metastasis development and long-term survival. Results Untargeted transcript profiling revealed high Decorin (Dcn) expression in CC1-L-expressing cells versus CT cells. Decorin was detected at the peri-endothelial layers of large blood vessels and in liver stellate cells. In metastatic lesions, it was expressed in pericyte-like cells covering capillary endothelium. Phosphokinase differential screening revealed reduced Ephrin type-A receptor 2 (EphA2) expression and activity in CC1-L- versus CT-expressing cells. Treatment of CT cells with recombinant Dcn led to decreased migration and invasion and decreased EphA2-mediated Erk and Akt signaling. CRC patients exhibiting high CC1 and DCN expression, in combination with low EPHA2 expression, benefit from longer 10-year survival than those with high EPHA2 expression. Conclusion CC1-L expression in poorly differentiated CRC inhibits liver metastasis through increased Decorin expression and EphA2-mediated signaling. Quadriplicate samples of each mouse colon cancer cell lines (control cells versus those expressing either short or long isoform of CEACAM1) have been used for RNA extraction
Project description:A combinatorial treatment consisting of a DNMTi and a LSD1i shows synergistic effects in reactivating aberrantly silenced genes by enriching H3K4me2 and H3K4me. 24 Samples consisting of 3 cell lines hybridised to the Illumina HumanHT-12 V4.0 Beadchip.
Project description:To study the interaction effects between promyelocytic leukemia (PML) gene knockdown and tumor necrosis factor-alpha (TNFalpha) signaling in human umbilical vein endothelial cells (HUVECs), we transfected control or two independent PML siRNAs into HUVEC cells without or with 20 ng/mL TNFalpha treatment for 20 h. The total RNA was extracted for gene expression microarray analyses. The experiment is a 3x2 two-factor design. One factor is siRNA and it has three levels (siCtrl, siPML1, siPML2). siCtrl is RISC-inducing non-targeting control siRNA. siPML1 and siPML2 designate two independent siRNAs against the PML gene. Two independent siRNAs were used to eliminate the off-target effects of siRNA. The other factor is TNFalpha treatment (20 ng/mL for 20 h) and it has two levels: Untreated (U) or Treated (T). Each sample has technical duplicates.
Project description:An eQTL analysis between DBA/2J and AKR/J mice strains on the ApoE null background was done in bone marrow derived macrophages and endothelial cells to identify modifier genes that affect atherosclerosis susceptibility. DBA/2J mice were crossed with AKR/J mice and their offspring crossed with each other to yield an F2 generation. Bone marrow derived macrophages were cultured and gene expression quantified using Illumina's MouseRef-8 v2 arrays in 170 F2 mice for an eQTL study. In addition primary endothelial cells derived from the aorta of 48 male F2 mice were also assayed using arrays for eQTL mapping. Lesion area in the aortic root was also quantified in these samples.
Project description:Demethylation treatment reduce gene body methylation as well as gene expression Total RNA obtained from untreated and treated cell lines were hybridised to the HumanHT12_V4 Human Expression Beadchip
Project description:Human disease mutation discovery has so far been biased towards protein coding regions. Having excluded all annotated coding regions, we performed targeted massively parallel re-sequencing of the non-repetitive genomic linkage interval of the MRX3 family at Xq28. We identified a regulatory mutation in the YY1 transcription factor binding site, which leads to overexpression of the chromatin-associated transcriptional regulator, HCFC1. When tested on embryonic murine neural stem cells (NSCs) and embryonic hippocampal neurons, HCFC1 overexpression led to a significant increase of the production of astrocytes and considerable reduction in neurite growth. Two other non-synonymous, potentially deleterious changes have been identified by X-exome sequencing in individuals with intellectual disability, implicating HCFC1 in normal brain function. Total RNA was extracted from LCL derived from four unrelated male controls, five unrelated female controls and two affected male cousins from the MRX3 family.